Contacts of the helix formed by residues 151 - 172 (chain F) in PDB entry 6DV9
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 ALA 151 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145F ALA* 3.7 1.9 - - - +
150F ILE* 1.3 81.4 - - - +
152F GLU* 1.3 67.7 + - - +
153F GLY 4.4 2.0 - - - +
154F THR* 3.3 27.7 + - - +
155F VAL* 3.5 14.7 - - - +
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Residues in contact with GLU 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR* 3.5 28.4 - - - +
142F ALA* 3.4 32.3 + - - +
145F ALA* 4.2 8.1 - - - +
151F ALA* 1.3 74.1 - - - +
153F GLY* 1.3 63.3 + - - +
155F VAL* 3.2 16.5 + - - +
156F LYS* 3.4 30.0 + - - +
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Residues in contact with GLY 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151F ALA* 4.4 2.0 - - - +
152F GLU* 1.3 77.7 - - - +
154F THR* 1.3 58.6 + - - +
155F VAL 3.3 0.2 - - - -
156F LYS* 3.2 18.9 + - - +
157F SER* 2.9 30.1 + - - -
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Residues in contact with THR 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F ILE* 3.9 17.2 - - + +
151F ALA* 3.3 32.2 + - - +
152F GLU 3.1 1.2 - - - -
153F GLY* 1.3 76.5 - - - +
155F VAL* 1.3 61.6 + - - +
157F SER* 2.9 20.8 + - - +
158F ARG* 3.1 39.7 + - + +
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Residues in contact with VAL 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 4.0 17.3 - - + -
141F THR* 4.1 13.2 - - + +
144F ILE* 3.9 24.5 - - + -
145F ALA* 3.7 24.2 - - + +
150F ILE* 3.6 22.2 - - + -
151F ALA 3.5 15.7 - - - +
152F GLU 3.2 5.8 + - - +
154F THR* 1.3 73.0 - - - +
156F LYS* 1.3 65.0 + - - +
158F ARG* 4.1 4.2 - - - +
159F LEU* 3.1 36.4 + - + +
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Residues in contact with LYS 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F THR* 3.7 18.4 - - + -
152F GLU* 3.6 38.1 - - - +
153F GLY* 3.2 17.1 + - - +
155F VAL* 1.3 78.1 - - - +
157F SER* 1.3 57.5 + - - +
159F LEU* 4.0 5.5 - - - +
160F HIS* 3.1 27.4 + - - +
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Residues in contact with SER 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F GLY 2.9 13.2 + - - -
154F THR* 2.9 21.7 + - - +
156F LYS* 1.3 76.5 - - - +
158F ARG* 1.3 65.9 + - - +
160F HIS* 3.2 7.6 + - - +
161F TYR* 3.1 23.2 + - - +
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Residues in contact with ARG 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126F GLU* 3.4 46.2 + - - +
127F HIS* 3.5 23.3 - - + +
130F VAL* 4.0 26.9 - - + +
148F LEU* 4.3 6.5 - - - +
150F ILE* 3.9 31.9 - - - +
154F THR* 3.1 37.6 + - + +
155F VAL 4.1 2.9 - - - +
157F SER* 1.3 80.2 + - - +
159F LEU* 1.3 58.3 + - - +
161F TYR* 3.3 1.3 + - - -
162F ALA* 2.8 34.1 + - - +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F VAL* 3.5 27.3 - - + +
131F ILE* 3.7 23.6 - - + -
134F SER* 3.9 26.0 - - - +
135F TYR* 4.1 12.1 - - + +
141F THR* 5.4 8.5 - - + +
144F ILE* 4.8 2.0 - - + -
155F VAL* 3.1 34.7 + - + +
156F LYS* 4.0 5.8 - - - +
158F ARG* 1.3 75.6 - - - +
160F HIS* 1.3 63.1 + - - +
162F ALA* 4.5 3.1 - - - -
163F VAL* 3.1 32.6 + - + +
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Residues in contact with HIS 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156F LYS 3.1 19.7 + - - +
157F SER* 3.5 8.7 - - - +
158F ARG 3.2 0.4 - - - -
159F LEU* 1.3 77.5 - - - +
161F TYR* 1.3 62.0 + - + +
163F VAL* 4.1 3.9 - - - +
164F ARG* 3.0 65.4 + - - +
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Residues in contact with TYR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 6.2 0.4 - - + -
127F HIS* 3.2 35.9 - + - +
157F SER 3.1 14.9 + - - +
158F ARG* 4.0 2.0 - - - +
160F HIS* 1.3 77.8 - - + +
162F ALA* 1.3 53.6 + - - +
163F VAL 3.1 2.0 - - - -
164F ARG* 2.8 17.2 + - + +
165F ALA* 2.6 58.4 + - + +
168F LEU* 5.9 3.1 - - - +
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Residues in contact with ALA 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 4.2 5.5 - - + +
127F HIS* 3.6 30.1 - - + +
130F VAL* 6.1 0.4 - - + -
131F ILE* 3.7 24.2 - - + -
158F ARG 2.8 24.0 + - - +
159F LEU 4.2 0.4 - - - +
161F TYR* 1.3 72.1 - - - +
163F VAL* 1.3 61.1 + - - +
165F ALA* 3.6 8.4 - - - +
166F LEU* 3.1 31.0 + - - +
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Residues in contact with VAL 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C LEU* 4.8 3.6 - - + -
823C ALA* 3.2 33.2 - - + +
824C ILE* 3.6 24.8 - - + +
131F ILE* 4.8 4.0 - - + -
135F TYR* 4.2 28.5 - - + +
159F LEU* 3.1 24.4 + - + +
160F HIS* 4.1 4.7 - - - +
162F ALA* 1.3 77.2 - - - +
164F ARG* 1.3 65.8 + - + +
166F LEU* 3.2 3.4 + - - -
167F ARG* 3.0 22.0 + - - +
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Residues in contact with ARG 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F HIS* 3.0 55.8 + - - +
161F TYR* 2.8 19.1 + - + +
163F VAL* 1.3 74.6 - - + +
165F ALA* 1.3 61.0 + - - +
167F ARG* 3.2 40.0 + - - +
168F LEU* 2.9 29.1 + - - +
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Residues in contact with ALA 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F LEU* 4.1 16.4 - - + -
161F TYR* 2.6 50.6 + - + +
162F ALA* 3.6 9.4 - - - +
164F ARG* 1.3 73.0 - - - +
166F LEU* 1.3 59.6 + - - +
168F LEU* 3.4 11.9 + - + +
169F THR* 3.0 27.1 + - - -
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Residues in contact with LEU 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
820C LEU* 3.9 31.9 - - + -
824C ILE* 3.9 17.7 - - + -
116F ILE* 5.7 2.2 - - + -
119F ALA* 3.3 42.4 - - + +
120F LEU* 3.9 17.7 - - + -
123F LEU* 3.6 20.9 - - + -
131F ILE* 4.9 4.5 - - + -
162F ALA 3.1 17.5 + - - +
163F VAL* 3.2 6.7 + - - +
165F ALA* 1.3 75.4 - - - +
167F ARG* 1.3 58.9 + - - +
169F THR* 3.1 4.6 + - - +
170F LEU* 2.8 34.7 + - + +
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Residues in contact with ARG 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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824C ILE* 3.2 31.8 + - - +
825C PHE* 4.5 20.3 + - + +
826C GLY* 4.6 6.3 - - - +
163F VAL* 3.0 15.3 + - - +
164F ARG* 3.2 51.7 + - - +
166F LEU* 1.3 75.0 - - - +
168F LEU* 1.3 57.8 + - - +
170F LEU* 4.5 4.9 - - - +
171F GLN* 3.0 60.0 + - + +
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Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F TYR* 5.9 3.1 - - - +
164F ARG 2.9 12.0 + - - +
165F ALA* 3.5 14.4 - - + +
167F ARG* 1.3 78.0 - - - +
169F THR* 1.3 65.5 + - - +
171F GLN* 4.0 4.0 - - - +
172F GLU* 3.1 54.7 + - + +
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Residues in contact with THR 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ASP 5.5 0.2 - - - -
119F ALA* 3.9 31.7 + - + +
122F GLN* 3.2 30.8 + - - +
123F LEU* 5.2 2.4 - - - +
165F ALA 3.0 13.5 + - - -
166F LEU* 3.1 8.0 + - - -
168F LEU* 1.3 80.9 - - - +
170F LEU* 1.3 64.1 + - + +
172F GLU* 3.7 7.5 + - - +
173F LEU* 3.5 33.1 + - + +
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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821C LEU* 5.2 3.8 - - + -
824C ILE* 3.6 28.0 - - + -
825C PHE* 4.2 11.2 - - + -
115F LEU* 4.3 18.2 - - + +
116F ILE* 4.5 9.6 - - + -
119F ALA* 4.0 23.1 - - + -
166F LEU* 2.8 23.9 + - + +
167F ARG* 4.1 4.3 - - - +
169F THR* 1.3 75.3 - - + +
171F GLN* 1.3 59.8 + - - +
173F LEU* 3.0 19.5 + - + -
174F GLY 3.1 0.2 + - - -
175F VAL* 3.0 59.0 + - + +
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Residues in contact with GLN 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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825C PHE* 4.8 13.0 - - + -
467D GLN* 5.6 0.5 + - - -
167F ARG* 3.0 47.5 + - + +
168F LEU* 4.2 3.6 - - - +
170F LEU* 1.3 75.5 - - - +
172F GLU* 1.3 61.4 + - + +
174F GLY* 3.3 12.2 + - - +
175F VAL 4.5 9.2 - - - +
177F ARG* 4.7 19.7 - - + +
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Residues in contact with GLU 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D GLN* 5.8 0.7 + - - -
168F LEU* 3.1 52.4 + - + +
169F THR* 3.9 9.5 - - - +
170F LEU 3.2 0.2 - - - -
171F GLN* 1.3 77.1 - - + +
173F LEU* 1.3 67.0 + - + +
174F GLY 3.5 0.2 - - - -
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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) + - + + + + + -
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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