Contacts of the helix formed by residues 160 - 175 (chain B) in PDB entry 4JVS
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 ASN 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B LEU* 3.9 27.4 - - + +
152B GLU* 3.0 21.0 + - - +
153B THR* 3.7 13.7 - - + -
158B ALA 4.0 1.4 + - - -
159B THR* 1.3 79.2 - - - +
161B VAL* 1.3 61.9 + - - +
163B GLN* 2.6 37.2 + - - +
164B SER* 2.9 29.3 + - - +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 3.5 46.7 - - + +
30B ARG* 3.8 27.8 - - + -
31B PHE* 4.0 7.9 - - + +
153B THR* 4.4 3.1 - - - -
154B SER 3.5 26.0 - - - +
155B ALA* 4.1 1.3 - - - -
158B ALA* 4.3 2.0 - - + -
159B THR 3.0 8.9 - - - +
160B ASN* 1.3 77.0 - - - +
162B GLU* 1.3 70.3 + - - +
164B SER* 3.4 7.1 + - - -
165B PHE* 3.2 29.9 - - + -
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Residues in contact with GLU 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PHE* 3.6 28.4 - - - +
51B ARG* 4.2 12.5 + - - -
161B VAL* 1.3 78.6 - - - +
163B GLN* 1.3 75.7 + - + +
164B SER 3.0 1.7 + - - -
165B PHE* 3.0 5.5 + - - +
166B MET* 3.0 45.9 + - + +
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Residues in contact with GLN 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151B LEU* 4.1 10.3 - - + -
160B ASN* 2.6 51.9 + - - +
161B VAL 3.7 0.5 + - - -
162B GLU* 1.3 87.4 + - + +
164B SER* 1.3 55.3 + - - +
166B MET* 4.6 5.6 - - - -
167B THR* 2.7 40.9 + - - +
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Residues in contact with SER 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 6.2 0.9 - - - -
88B ILE* 4.6 4.0 - - - +
120B LEU* 3.3 30.7 - - - +
122B VAL* 3.9 8.9 - - - +
151B LEU* 3.5 14.0 - - - +
153B THR* 3.3 19.6 - - - +
160B ASN 2.9 20.3 + - - -
161B VAL* 3.7 7.0 - - - -
162B GLU 3.0 0.4 + - - -
163B GLN* 1.3 77.6 - - - +
165B PHE* 1.3 66.6 - - - +
167B THR* 3.8 0.7 - - - -
168B MET* 3.2 18.2 + - - +
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.9 23.5 - - + +
16B LEU* 3.7 34.5 - - + -
27B LEU* 4.0 14.4 - - + -
28B LEU* 4.4 8.5 - - - -
31B PHE* 3.5 58.3 - + + -
62B LEU* 5.1 1.6 - - + +
64B ILE* 3.9 17.0 - - + -
88B ILE* 3.9 14.8 - - + -
161B VAL* 3.2 27.6 - - + -
162B GLU 3.0 2.0 + - - -
164B SER* 1.3 79.9 - - - +
166B MET* 1.3 62.4 + - - +
168B MET* 3.4 6.7 + - - +
169B ALA* 2.9 29.5 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 3.5 25.1 - - + -
51B ARG* 3.7 6.3 - - - +
53B ILE* 3.5 51.4 - - + -
54B GLU 5.8 2.0 - - - +
55B LEU* 4.8 10.0 - - + +
62B LEU* 4.8 0.2 - - + -
162B GLU* 3.0 40.5 + - + +
163B GLN* 4.3 4.7 - - - +
165B PHE* 1.3 75.6 - - - +
167B THR* 1.3 64.9 + - - +
169B ALA* 3.9 2.2 - - - +
170B ALA* 3.0 25.1 + - - +
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Residues in contact with THR 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B LEU* 4.6 16.6 - - + -
149B PRO* 4.6 11.9 - - + -
151B LEU* 4.5 7.7 - - + +
163B GLN* 2.7 27.2 + - - +
164B SER* 3.8 5.8 - - - +
166B MET* 1.3 77.4 - - - +
168B MET* 1.3 59.0 + - - +
170B ALA* 3.3 7.0 + - - +
171B GLU* 3.0 45.6 + - + +
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Residues in contact with MET 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.2 17.0 - - + -
86B GLY* 3.5 30.3 - - - +
87B ILE 3.8 2.0 - - - -
88B ILE* 4.1 16.8 - - + -
118B ASN* 3.6 39.7 - - + +
119B LYS 3.8 17.3 - - - +
120B LEU* 4.2 9.6 - - + -
149B PRO* 5.9 0.9 - - + -
164B SER 3.2 16.1 + - - +
165B PHE* 3.7 4.7 - - - +
166B MET 3.3 0.2 - - - -
167B THR* 1.3 83.4 - - - +
169B ALA* 1.3 62.0 + - - +
171B GLU* 3.5 6.3 + - + +
172B ILE* 3.1 37.7 + - + +
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Residues in contact with ALA 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.3 21.2 - - + -
14B LEU* 5.7 0.7 - - + -
53B ILE* 3.9 27.8 - - + -
55B LEU* 4.0 8.3 - - + -
62B LEU* 4.3 15.7 - - + -
165B PHE 2.9 17.1 + - - +
166B MET* 3.9 4.7 - - - +
168B MET* 1.3 74.5 - - - +
170B ALA* 1.3 60.6 + - - +
172B ILE* 3.4 1.2 + - - -
173B LYS* 3.0 27.7 + - - +
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU* 3.8 19.2 - - + +
56B ASP* 5.9 2.2 - - - +
166B MET 3.0 17.7 + - - +
167B THR* 3.5 7.4 - - - +
169B ALA* 1.3 78.1 - - - +
171B GLU* 1.3 63.3 + - - +
173B LYS* 3.3 5.7 + - - +
174B LYS* 3.0 28.2 + - - +
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Residues in contact with GLU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 3.2 26.9 + - + +
149B PRO* 5.2 10.8 - - + -
167B THR* 3.0 33.3 + - + +
168B MET* 3.8 9.2 - - + +
170B ALA* 1.3 82.2 - - - +
172B ILE* 1.3 62.2 + - - +
174B LYS* 2.6 42.0 + - - +
175B ARG* 3.2 18.2 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.8 26.4 - - + -
14B LEU* 3.8 14.6 - - + -
85B HIS* 3.5 45.1 - - + +
86B GLY* 3.7 17.7 - - - +
118B ASN* 3.8 17.9 - - + +
168B MET* 3.1 30.1 + - + +
169B ALA 3.8 3.6 - - - +
171B GLU* 1.3 72.4 - - - +
173B LYS* 1.3 65.7 + - - +
175B ARG* 3.3 23.2 + - - +
176B MET* 3.5 5.9 + - - -
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR* 4.3 24.5 + - + +
12B PHE* 3.8 14.6 - - + -
55B LEU* 3.9 28.0 - - + -
56B ASP* 3.3 29.9 + - - +
58B LYS* 4.5 13.5 - - - -
60B ILE* 4.0 16.6 - - + -
169B ALA 3.0 18.4 + - - +
170B ALA* 3.3 6.5 + - - +
172B ILE* 1.3 77.7 - - - +
174B LYS* 1.3 57.9 + - - +
176B MET* 2.9 26.1 + - - +
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Residues in contact with LYS 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ALA 3.0 15.9 + - - +
171B GLU* 2.6 43.1 + - - +
172B ILE 3.2 0.2 - - - -
173B LYS* 1.3 74.0 - - - +
175B ARG* 1.3 56.6 + - - +
176B MET* 2.9 28.1 + - - +
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Residues in contact with ARG 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ALA 5.4 0.2 + - - -
85B HIS* 3.3 40.4 + - - +
114B SER* 5.3 2.6 + - - -
116B ASN* 3.0 45.3 + - - +
117B VAL* 4.5 2.2 - - - +
118B ASN* 2.7 22.4 + - - +
171B GLU 3.2 11.0 + - - +
172B ILE* 3.4 19.2 + - - +
174B LYS* 1.3 74.5 - - - +
176B MET* 1.3 67.4 + - - +
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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