Contacts of the helix formed by residues 144 - 168 (chain R) in PDB entry 6VMS
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 144 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLU* 6.0 2.2 - - + +
31A ALA* 5.0 17.4 + - + +
32A ARG* 5.9 6.3 - - + +
140R MET 3.6 14.9 + - - -
141R LEU* 3.1 21.4 + - + +
142R TYR 4.3 1.0 + - - -
143R ASN* 1.3 75.6 - - - +
145R ARG* 1.3 58.8 + - - +
146R TYR* 3.1 23.5 + - + +
147R SER* 4.0 15.7 - - - +
148R SER* 2.6 34.1 + - - -
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Residues in contact with ARG 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 2.8 42.9 + - - +
334B SER* 5.6 2.0 + - - -
143R ASN 3.5 5.8 + - - +
144R THR* 1.3 73.4 - - - +
146R TYR* 1.3 104.6 + - + +
147R SER 3.4 0.6 + - - -
148R SER* 4.0 6.7 - - - -
149R LYS* 3.7 22.3 + - - +
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Residues in contact with TYR 146 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 4.2 30.3 + - + +
27A GLY* 4.1 21.9 + - - -
28A GLU* 3.8 35.3 - - + +
31A ALA* 4.1 12.1 - - + +
55B LEU* 3.5 32.6 - - + +
144R THR* 3.1 17.2 - - + -
145R ARG* 1.3 127.3 + - + +
147R SER* 1.3 56.8 + - - +
149R LYS* 4.9 2.5 - - - +
150R ARG* 5.2 5.0 + - - +
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Residues in contact with SER 147 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141R LEU* 4.5 9.0 + - - +
144R THR* 3.4 20.0 + - - +
146R TYR* 1.3 79.2 - - - +
148R SER* 1.3 62.8 + - - +
149R LYS 3.3 2.0 - - - -
150R ARG* 3.0 24.2 + - - +
151R ARG* 2.9 35.9 + - - +
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Residues in contact with SER 148 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 3.6 20.7 + - - -
141R LEU 3.8 2.4 + - - -
143R ASN* 4.0 3.8 + - - -
144R THR 2.6 37.2 + - - -
145R ARG* 4.3 4.0 - - - -
146R TYR 3.8 0.2 - - - -
147R SER* 1.3 74.9 + - - +
149R LYS* 1.3 65.9 + - - +
151R ARG* 3.2 27.3 + - - +
152R VAL* 2.9 28.5 + - - +
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Residues in contact with LYS 149 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145R ARG 3.7 17.6 + - - +
146R TYR 5.3 2.5 - - - +
147R SER 3.3 0.4 - - - -
148R SER* 1.3 76.7 - - - +
150R ARG* 1.3 57.8 + - - +
152R VAL* 3.2 9.2 - - + +
153R THR* 2.8 40.3 + - - +
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Residues in contact with ARG 150 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R TYR 5.2 2.9 + - - +
147R SER* 3.0 25.2 + - - +
149R LYS* 1.3 77.0 - - - +
151R ARG* 1.3 61.9 + - - +
153R THR* 3.3 6.5 + - - -
154R VAL* 2.9 46.9 + - + +
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Residues in contact with ARG 151 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 3.0 31.4 + - - +
130R ILE* 6.2 1.3 - - - -
131R ASP* 3.2 25.7 + - - -
134R THR* 4.5 24.6 - - - +
141R LEU* 4.3 12.2 + - - +
142R TYR* 4.4 11.7 - - - +
147R SER* 2.9 17.9 + - - +
148R SER* 3.2 34.8 + - - +
150R ARG* 1.3 78.3 - - - +
152R VAL* 1.3 55.1 + - - +
154R VAL* 3.4 6.8 + - - +
155R MET* 3.0 42.2 + - + +
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Residues in contact with VAL 152 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 3.9 33.7 - - + +
71R TYR* 4.3 14.8 - - + -
72R LEU* 4.0 13.0 - - + -
148R SER 2.9 14.7 + - - +
149R LYS* 3.2 17.9 - - + +
151R ARG* 1.3 74.1 - - - +
153R THR* 1.3 73.1 + - - +
155R MET* 3.9 6.9 - - - +
156R ILE* 2.9 51.3 + - + +
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Residues in contact with THR 153 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R LYS* 2.8 29.6 + - - +
150R ARG* 3.7 7.9 - - + -
152R VAL* 1.3 79.3 - - - +
154R VAL* 1.3 60.2 + - + +
156R ILE* 4.0 5.6 - - - +
157R SER* 2.9 36.6 + - - +
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Residues in contact with VAL 154 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150R ARG* 2.9 33.7 + - + +
151R ARG* 3.6 8.1 - - + +
153R THR* 1.3 79.1 - - + +
155R MET* 1.3 61.5 + - + +
157R SER* 2.9 6.7 + - - -
158R ILE* 2.9 54.9 + - + +
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Residues in contact with MET 155 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R THR* 4.8 1.1 - - + -
72R LEU* 4.1 19.3 - - + -
127R ALA* 3.5 45.8 - - + +
130R ILE* 3.9 21.1 - - + -
131R ASP* 4.1 17.5 - - + +
151R ARG* 3.0 40.9 + - + +
152R VAL* 3.3 6.3 + - - +
154R VAL* 1.3 80.5 - - + +
156R ILE* 1.3 57.6 + - - +
158R ILE* 3.4 6.9 + - + +
159R VAL* 2.9 35.6 + - - +
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Residues in contact with ILE 156 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R TYR* 4.5 11.2 - - + +
72R LEU* 3.4 21.8 - - + -
75R SER* 3.7 26.0 - - - +
124R ASN* 4.9 1.3 - - - +
152R VAL* 2.9 40.1 + - + +
153R THR* 4.1 4.0 - - - +
155R MET* 1.3 77.3 - - - +
157R SER* 1.3 63.0 + - - +
159R VAL* 3.2 5.8 + - - +
160R TRP* 3.0 44.4 + - + +
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Residues in contact with SER 157 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153R THR* 2.9 25.6 + - - +
154R VAL* 2.9 13.2 + - - -
156R ILE* 1.3 78.7 - - - +
158R ILE* 1.3 65.2 + - - +
160R TRP* 4.6 3.1 - - - +
161R VAL* 2.9 36.5 + - - +
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Residues in contact with ILE 158 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R VAL* 2.9 48.3 + - + +
155R MET* 3.7 8.1 - - + +
157R SER* 1.3 78.4 + - - +
159R VAL* 1.3 61.5 + - + +
161R VAL* 4.1 3.3 - - - +
162R LEU* 2.9 47.7 + - + +
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Residues in contact with VAL 159 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120R ALA* 3.5 28.9 - - + +
123R LEU* 3.5 38.5 - - + +
124R ASN* 3.1 31.0 - - - +
127R ALA* 4.5 5.8 - - + -
155R MET 2.9 23.0 + - - +
156R ILE 3.2 4.0 + - - +
158R ILE* 1.3 78.9 - - + +
160R TRP* 1.3 66.3 + - + +
162R LEU* 3.9 1.0 - - - +
163R SER* 2.9 24.9 + - - -
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Residues in contact with TRP 160 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75R SER* 4.0 30.7 + - - -
78R VAL* 4.7 8.1 - - + -
79R ALA* 3.7 20.0 - - + -
82R LEU* 4.3 8.5 - - + -
116R MET* 4.3 15.7 - - + +
117R MET* 3.5 39.5 - - + -
120R ALA* 3.8 17.7 - - + -
124R ASN* 4.8 3.6 - - - +
156R ILE* 3.0 46.2 + - + +
157R SER* 4.2 3.6 - - - +
159R VAL* 1.3 80.2 - - + +
161R VAL* 1.3 59.4 + - + +
163R SER* 2.6 23.5 + - - -
164R PHE* 2.9 17.2 + - - +
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Residues in contact with VAL 161 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157R SER* 2.9 26.8 + - - +
158R ILE* 4.1 2.9 - - - +
160R TRP* 1.3 76.6 - - + +
162R LEU* 1.3 61.4 + - - +
164R PHE* 3.3 5.8 + - - +
165R THR* 2.8 40.9 + - - +
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Residues in contact with LEU 162 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119R THR* 5.6 1.1 - - + -
123R LEU* 3.8 27.1 - - + -
158R ILE* 2.9 31.5 + - + +
159R VAL 4.0 2.0 - - - +
161R VAL* 1.3 76.7 - - - +
163R SER* 1.3 62.3 + - - +
165R THR* 3.7 10.7 - - + -
166R ILE* 2.9 29.0 + - + +
196R VAL* 4.3 28.9 - - + +
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Residues in contact with SER 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R MET* 3.4 34.0 + - - +
119R THR* 3.7 16.3 - - - +
120R ALA* 3.9 6.6 - - - +
159R VAL 2.9 14.9 + - - -
160R TRP* 2.6 31.4 + - - -
162R LEU* 1.3 76.7 - - - +
164R PHE* 1.3 62.7 + - - +
166R ILE* 2.9 25.1 - - - +
167R SER* 2.9 12.7 + - - -
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Residues in contact with PHE 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R THR* 6.1 2.0 - - + -
116R MET* 3.4 33.7 - - + -
160R TRP 2.9 12.6 + - - +
161R VAL* 3.8 6.3 - - - +
163R SER* 1.3 81.4 + - - +
165R THR* 1.3 63.7 + - - +
167R SER* 2.9 20.8 + - - -
168R CYS* 2.9 29.6 + - + +
171R LEU* 4.6 20.4 - - + -
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Residues in contact with THR 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161R VAL* 2.8 32.5 + - - +
162R LEU* 3.7 13.2 - - + -
164R PHE* 1.3 82.2 - - - +
166R ILE* 1.3 63.3 + - - +
168R CYS* 3.4 7.8 + - + +
169R PRO* 3.3 17.2 - - - +
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Residues in contact with ILE 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115R VAL* 4.8 5.8 - - + -
119R THR* 4.1 18.4 - - + +
162R LEU* 2.9 19.5 + - + +
163R SER* 2.9 28.3 - - - +
165R THR* 1.3 78.5 - - - +
167R SER* 1.3 58.1 + - - +
169R PRO* 3.1 17.4 - - + +
189R PHE* 3.7 16.1 - - + -
193R SER* 3.0 42.4 - - - +
196R VAL* 4.9 19.5 - - + -
197R SER* 4.1 7.6 - - - +
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Residues in contact with SER 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R THR* 3.7 37.8 - - - +
115R VAL* 4.4 11.7 - - - -
116R MET* 3.6 17.8 - - - +
163R SER 2.9 15.3 + - - -
164R PHE* 2.9 24.6 + - - -
166R ILE* 1.3 78.4 - - - +
168R CYS* 1.3 65.4 + - - +
169R PRO* 3.3 0.4 - - - -
170R LEU* 3.1 23.6 + - - +
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Residues in contact with CYS 168 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112R THR* 5.2 0.2 - - - -
164R PHE* 2.9 26.5 + - + +
165R THR* 3.6 9.0 - - + +
167R SER* 1.3 76.3 + - - +
169R PRO* 1.3 61.5 - - + +
171R LEU* 2.7 58.5 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il