Contacts of the helix formed by residues 157 - 175 (chain B) in PDB entry 7V3X
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 SER 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A ARG* 6.0 3.8 - - - -
156B ALA* 1.3 69.2 - - - +
158B SER* 1.3 63.9 + - - +
160B VAL* 4.1 8.2 - - - +
161B ARG* 3.2 27.5 + - - +
194B TYR* 4.0 28.8 - - - -
196B VAL* 4.6 6.0 - - - +
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Residues in contact with SER 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A GLN* 3.2 46.1 - - - +
156B ALA* 3.1 3.5 + - - -
157B SER* 1.3 82.4 + - - +
159B VAL* 1.3 65.2 + - - +
161B ARG* 4.5 3.1 - - - +
162B ARG* 3.7 31.5 + - - +
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ALA* 2.8 33.6 + - + +
158B SER* 1.3 74.0 - - - +
160B VAL* 1.3 64.3 + - + +
161B ARG 3.3 1.6 - - - -
162B ARG* 3.3 36.3 + - - +
163B GLU* 3.3 16.8 + - + +
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Residues in contact with VAL 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL 5.7 4.5 - - - +
148B THR* 6.3 0.9 - - + -
151B PHE* 4.6 14.6 - - + -
156B ALA 3.0 24.0 + - - +
157B SER* 3.4 5.3 + - - +
159B VAL* 1.3 76.1 - - + +
161B ARG* 1.3 58.2 + - - +
163B GLU* 4.3 3.3 - - - +
164B LEU* 3.0 37.6 + - + +
194B TYR* 3.9 51.6 - - + -
196B VAL* 5.4 2.7 - - + -
197B GLU* 4.9 10.8 - - + +
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Residues in contact with ARG 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 5.6 6.7 - - - +
146A SER* 4.5 1.2 + - - -
148A THR* 4.7 4.4 - - - +
149A SER* 3.6 39.5 - - - +
183A GLU* 2.6 37.8 + - - -
193A ARG* 4.7 5.1 - - - +
157B SER 3.2 16.8 + - - +
158B SER* 4.5 3.4 - - - +
160B VAL* 1.3 75.1 - - - +
162B ARG* 1.3 55.8 + - - +
164B LEU* 3.7 4.4 - - - +
165B PHE* 2.6 41.1 + - + +
196B VAL* 4.0 21.3 + - + +
197B GLU 5.9 0.2 - - - +
199B PHE* 3.3 26.2 + - - +
200B VAL* 3.5 24.1 - - + +
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Residues in contact with ARG 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A PRO* 5.9 7.9 - - + -
152A GLN* 5.0 8.3 - - - +
158B SER* 3.7 29.9 + - - +
159B VAL* 3.3 31.6 + - - +
161B ARG* 1.3 78.0 - - - +
163B GLU* 1.3 57.0 + - - +
165B PHE* 3.4 9.1 - - - +
166B ARG* 2.9 28.3 + - - +
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Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LEU* 5.2 14.6 - - + -
159B VAL* 3.3 15.5 + - + +
160B VAL* 4.4 3.4 - - - +
162B ARG* 1.3 74.0 - - - +
164B LEU* 1.3 55.9 + - - +
166B ARG* 2.9 12.8 + - - +
167B LEU* 2.8 34.8 + - - +
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Residues in contact with LEU 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B VAL* 6.1 4.5 - - + +
160B VAL* 3.0 28.3 + - + +
161B ARG* 3.7 5.4 - - - +
163B GLU* 1.3 75.6 - - - +
165B PHE* 1.3 56.8 - - - +
167B LEU* 3.4 6.8 + - - +
168B VAL* 3.1 31.2 + - - +
180B MET* 4.8 8.6 - - + +
197B GLU* 5.5 11.4 - - + -
200B VAL* 4.2 12.2 - - + +
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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
----------------------------------------------------------
76A PHE 4.9 0.4 - - - -
77A GLU* 3.9 44.2 - - + -
109A SER* 4.7 3.8 - - - -
110A PRO* 4.2 37.5 - - + -
111A ASP 5.0 5.4 - - - -
112A PRO* 5.2 5.2 - - + -
161B ARG* 2.6 26.6 + - + +
162B ARG* 3.4 8.7 - - - +
164B LEU* 1.3 70.4 - - - +
166B ARG* 1.3 60.5 + - + +
168B VAL* 3.8 0.7 - - - +
169B ALA* 2.8 54.5 + - + +
200B VAL* 3.8 28.4 - - + +
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Residues in contact with ARG 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A ASP 4.7 3.1 - - - +
112A PRO* 3.6 35.9 + - + +
123B LEU* 4.6 21.5 - - + +
124B SER* 4.4 22.2 + - - +
162B ARG 2.9 15.3 + - - +
163B GLU* 2.9 13.9 + - - +
165B PHE* 1.3 79.5 - - + +
167B LEU* 1.3 52.1 + - - +
169B ALA* 3.5 5.1 - - - +
170B ARG* 2.7 38.0 + - - +
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Residues in contact with LEU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ILE* 6.1 3.8 - - - -
144B ILE* 6.0 2.0 - - + -
147B VAL* 5.9 4.5 - - + -
163B GLU 2.8 14.8 + - - +
164B LEU* 3.6 11.0 - - - +
166B ARG* 1.3 73.1 - - - +
168B VAL* 1.3 63.5 + - - +
170B ARG* 3.1 7.4 + - - +
171B LEU* 3.0 34.4 + - + +
180B MET* 5.0 8.3 - - + -
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 3.9 25.3 + - - +
164B LEU 3.1 13.8 + - - +
165B PHE 4.1 1.8 - - - +
167B LEU* 1.3 77.8 - - - +
169B ALA* 1.3 58.9 + - - +
171B LEU* 3.5 13.1 + - - +
172B LYS* 3.2 21.7 + - - +
180B MET* 4.4 9.5 - - + +
200B VAL* 4.2 18.6 - - + +
201B SER* 5.1 1.8 - - - +
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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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112A PRO* 4.2 19.5 - - + -
165B PHE* 2.8 45.5 + - + +
166B ARG 3.5 3.8 - - - +
168B VAL* 1.3 69.2 - - - +
170B ARG* 1.3 68.6 + - - +
172B LYS* 3.3 19.2 + - - +
173B GLN* 3.5 14.3 + - - +
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PRO* 4.8 5.5 - - + +
127B ILE* 4.9 16.6 - - + -
166B ARG 2.7 18.3 + - - +
167B LEU* 3.2 12.3 - - - +
169B ALA* 1.3 70.7 - - - +
171B LEU* 1.3 54.9 + - + +
173B GLN* 2.9 35.9 + - - +
174B ILE* 3.2 20.2 + - + +
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Residues in contact with LEU 171 (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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41B SER* 5.4 2.5 - - - -
130B ILE* 4.4 20.6 - - + -
134B ILE* 4.5 7.4 - - + -
142B VAL* 4.2 22.0 - - + -
144B ILE* 3.8 23.3 - - + -
167B LEU* 3.0 29.4 + - + +
168B VAL* 3.7 11.2 - - - +
169B ALA 3.3 0.2 - - - -
170B ARG* 1.3 75.8 - - + +
172B LYS* 1.3 56.5 + - - +
174B ILE* 3.3 11.2 + - + +
175B GLY 3.0 22.7 + - - -
176B ALA* 3.5 14.5 + - + +
178B THR* 3.7 29.8 - - + +
180B MET* 4.6 4.0 - - - -
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Residues in contact with LYS 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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82A ASP* 5.7 4.7 - - - +
39B GLY* 3.8 21.9 - - - +
40B ARG* 5.9 1.6 - - - +
168B VAL 3.2 12.3 + - - +
169B ALA* 3.4 13.5 - - - +
170B ARG 3.2 0.6 - - - -
171B LEU* 1.3 75.8 - - - +
173B GLN* 1.3 62.3 + - + +
175B GLY* 3.2 15.6 + - - -
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Residues in contact with GLN 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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112A PRO* 3.5 34.4 - - - +
169B ALA* 3.5 12.0 + - - +
170B ARG* 2.9 12.5 + - - +
172B LYS* 1.3 77.6 - - + +
174B ILE* 1.3 68.6 + - + +
175B GLY* 3.2 1.6 + - - -
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Residues in contact with ILE 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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130B ILE* 6.5 0.4 - - + -
131B ASN* 4.6 24.5 - - + +
134B ILE* 3.8 42.5 - - + +
170B ARG* 3.4 20.6 - - + +
171B LEU* 3.5 15.9 - - + +
173B GLN* 1.3 79.4 - - + +
175B GLY* 1.3 60.5 + - - +
176B ALA* 4.7 4.5 - - + -
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Residues in contact with GLY 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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38B ILE* 5.9 2.8 - - - +
39B GLY* 4.5 11.7 - - - -
140B ARG* 5.3 2.1 - - - +
171B LEU 3.0 5.1 + - - -
172B LYS 3.2 13.2 + - - -
173B GLN 3.1 3.7 - - - -
174B ILE* 1.3 79.4 - - - +
176B ALA* 1.3 59.2 + - - +
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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
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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