Contacts of the helix formed by residues 154 - 163 (chain O) in PDB entry 6N1H
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 154 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152O GLU* 2.8 15.8 + - - +
153O PRO* 1.3 74.5 - - + +
155O ASN* 1.3 55.1 - - - +
156O PRO* 4.4 5.3 - - - +
157O SER* 2.8 43.0 + - - -
158O LYS* 3.5 2.5 + - - +
144P GLU 4.3 4.5 - - - +
147P GLN* 3.0 13.9 - - - +
148P ALA* 2.6 54.5 - - + +
151P ALA* 6.0 0.7 - - + -
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Residues in contact with ASN 155 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O ILE 4.9 0.4 - - - -
126O VAL 3.9 7.8 + - - +
127O THR* 3.4 38.2 + - - +
129O VAL* 3.3 23.4 + - - +
130O GLU* 5.4 2.6 + - - +
153O PRO 3.3 6.3 + - - +
154O THR* 1.3 69.9 - - - +
156O PRO* 1.4 60.8 - - + +
157O SER 3.4 0.2 + - - -
158O LYS* 3.4 21.6 + - - +
159O MET* 3.7 11.1 + - - +
147P GLN* 3.1 25.5 + - - +
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Residues in contact with PRO 156 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123O ILE* 3.3 39.4 - - + +
124O ALA* 4.4 10.5 - - - +
126O VAL 5.9 0.4 - - - +
154O THR* 3.7 7.4 - - - +
155O ASN* 1.4 74.6 - - + +
157O SER* 1.3 56.9 + - - +
159O MET* 3.3 2.5 + - - +
160O ARG* 3.1 31.4 + - - +
143P ASP* 4.9 2.5 - - - +
144P GLU* 3.7 31.9 - - + +
147P GLN* 2.3 37.7 - - + +
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Residues in contact with SER 157 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150L ARG* 4.4 11.3 + - - -
151O ALA 5.0 0.7 - - - -
152O GLU* 3.3 30.7 + - - +
154O THR* 2.8 31.5 + - - -
156O PRO* 1.3 71.8 - - - +
158O LYS* 1.3 60.3 + - - +
159O MET 3.3 0.2 - - - -
160O ARG* 3.6 15.0 - - - +
161O LYS* 3.1 26.2 + - - +
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Residues in contact with LYS 158 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O VAL* 3.8 23.0 - - + +
130O GLU* 5.6 10.3 + - + +
133O LEU* 5.9 1.1 - - + -
149O VAL* 3.3 39.7 - - + +
150O ARG* 4.5 11.8 - - + +
151O ALA* 3.7 20.2 - - - +
153O PRO* 4.5 19.3 + - - +
154O THR 4.3 5.8 - - - +
155O ASN* 3.4 21.8 + - - +
156O PRO 3.2 0.2 - - - -
157O SER* 1.3 78.4 - - - +
159O MET* 1.3 58.4 + - - +
161O LYS* 3.6 0.6 + - - -
162O LEU* 3.1 21.3 + - - +
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Residues in contact with MET 159 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122O LEU* 3.3 31.4 - - + +
123O ILE* 3.8 12.6 - - + +
126O VAL* 3.9 21.5 - - + +
129O VAL* 3.7 36.1 - - + -
132O LEU* 5.8 3.6 - - + -
155O ASN 3.7 5.8 + - - +
156O PRO 3.3 8.6 + - - +
157O SER 3.3 0.2 - - - -
158O LYS* 1.3 78.0 - - - +
160O ARG* 1.3 55.2 + - - +
161O LYS 3.2 0.2 - - - -
162O LEU* 3.0 23.0 + - + +
163O PHE* 2.7 65.0 + - + -
177O LEU* 5.5 6.1 - - + -
181O LEU* 5.6 2.7 - - + -
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Residues in contact with ARG 160 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130L GLU* 2.4 51.1 + - - +
131L TRP* 3.6 13.7 - - - +
134L ASP* 1.7 46.2 + - - -
146L TYR* 3.7 6.0 + - - +
150L ARG* 3.6 41.2 + - - +
119O ARG* 4.6 3.0 + - - +
123O ILE* 3.7 28.3 - - + +
156O PRO* 3.1 18.4 + - - +
157O SER* 3.8 13.1 - - - +
158O LYS 3.4 0.4 - - - -
159O MET* 1.3 75.9 - - - +
161O LYS* 1.3 60.8 + - - +
163O PHE* 4.0 4.0 - - - +
164O SER* 3.2 20.4 + - - -
144P GLU* 4.3 12.3 - - - +
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Residues in contact with LYS 161 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L ARG* 4.9 7.7 - - - +
148O ALA* 3.4 33.1 - - + +
149O VAL* 3.7 17.5 - - + -
152O GLU* 4.1 22.9 + - - +
157O SER 3.1 17.0 + - - +
158O LYS* 4.0 5.4 - - - +
160O ARG* 1.3 76.2 - - - +
162O LEU* 1.3 63.2 + - - +
164O SER* 3.3 17.8 + - - +
165O PHE* 3.2 37.0 - - + -
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Residues in contact with LEU 162 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O ILE* 6.5 0.2 - - + -
129O VAL* 4.7 4.3 - - + -
132O LEU* 5.1 10.5 - - + +
133O LEU* 3.7 28.7 - - + +
136O LEU* 5.8 0.7 - - + -
141O LEU* 4.9 7.9 - - + -
149O VAL* 4.3 8.3 - - + +
158O LYS 3.1 17.6 + - - +
159O MET* 3.0 36.7 + - + +
161O LYS* 1.3 77.6 - - - +
163O PHE* 1.3 70.0 + - + +
164O SER 3.4 0.5 + - - -
165O PHE* 3.4 15.0 + - - +
166O THR* 3.7 7.4 + - - -
169O TRP* 4.3 13.4 - - + -
177O LEU* 3.7 32.8 - - + -
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Residues in contact with PHE 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O ILE* 3.6 34.8 - - + -
116O ASP* 5.4 2.5 - - - -
119O ARG* 3.7 46.3 + - + +
122O LEU* 3.7 31.0 - - + -
123O ILE* 3.8 26.2 - - + -
159O MET* 2.7 52.9 + - + +
160O ARG 4.4 0.4 - - - +
162O LEU* 1.3 75.5 - - + +
164O SER* 1.3 63.8 + - - +
165O PHE 3.2 1.3 - - - -
166O THR* 3.2 27.9 + - - -
167O PRO* 3.4 11.6 - - - +
169O TRP* 6.3 0.4 - + - -
177O LEU* 5.9 1.8 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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