Contacts of the helix formed by residues 158 - 169 (chain B) in PDB entry 5FV7
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 GLU 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86B ASP* 3.7 4.9 - - - +
89B PRO* 3.6 24.2 - - + +
90B PRO* 3.8 6.6 - - + +
155B ALA* 4.3 1.1 - - - -
157B SER* 1.3 81.8 - - - +
159B ALA* 1.3 66.8 + - - +
160B GLU* 3.3 25.1 - - - +
161B ALA* 3.1 26.9 + - + +
162B SER* 3.4 7.4 + - - -
181B ASP* 5.5 0.3 - - - -
185B PHE* 3.2 15.0 - - + -
234B TYR* 2.6 37.0 + - - +
287B GLU 4.4 2.0 + - - +
1336B MG 4.4 4.0 - - - -
1337B MG 4.6 3.4 - - - -
1338B R3Z 4.6 1.8 - - - +
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Residues in contact with ALA 159 (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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34B ASP* 3.5 13.9 - - - +
36B SER* 5.5 0.4 - - - +
84B VAL* 3.4 30.1 - - + +
85B PHE 3.8 10.8 - - - -
86B ASP* 2.6 22.4 + - - +
155B ALA* 3.9 11.2 - - - -
157B SER 3.7 1.6 + - - -
158B GLU* 1.3 71.6 - - - +
160B GLU* 1.3 58.0 + - - +
162B SER* 2.9 6.9 + - - -
163B CYS* 2.8 30.2 + - - -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B ASP* 3.3 14.8 + - - +
158B GLU* 3.3 22.6 - - - +
159B ALA* 1.3 78.2 - - - +
161B ALA* 1.3 63.6 + - - +
163B CYS* 3.4 10.7 - - - +
164B ALA* 3.1 18.0 + - - +
177B THR* 4.8 4.0 - - + -
179B ASP* 3.0 13.3 - - - +
181B ASP* 2.9 16.8 - - - +
182B CYS* 3.4 29.0 - - + +
185B PHE* 3.8 9.6 - - + -
1336B MG 1.9 31.7 - - - -
1337B MG 2.6 21.1 - - - -
1338B R3Z 2.7 2.8 + - - -
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Residues in contact with ALA 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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158B GLU* 3.1 16.0 + - + +
160B GLU* 1.3 80.6 - - - +
162B SER* 1.3 57.5 + - - +
164B ALA* 3.2 6.4 + - - +
165B ALA* 2.9 22.7 + - - +
168B LYS* 5.7 0.3 + - - -
185B PHE* 3.7 42.8 - - + +
286B PRO* 4.2 6.2 - - + +
287B GLU 4.5 3.4 - - - +
288B VAL* 3.5 22.9 - - + +
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.0 4.5 - - - -
155B ALA* 3.4 21.5 - - - +
156B PRO* 3.8 2.9 - - - +
158B GLU 3.4 4.2 + - - -
159B ALA 2.9 9.5 + - - -
161B ALA* 1.3 76.3 - - - +
163B CYS* 1.3 64.9 + - - +
165B ALA* 3.3 5.6 + - - +
166B LEU* 3.0 30.1 + - - +
287B GLU 4.4 0.7 + - - -
288B VAL* 3.8 12.0 - - - +
289B LEU* 3.6 39.8 + - - +
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Residues in contact with CYS 163 (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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32B ALA* 4.1 21.6 - - + +
34B ASP* 4.2 22.9 - - - -
84B VAL* 3.9 22.2 - - - -
159B ALA 2.8 18.5 + - - -
160B GLU* 3.4 16.2 - - - +
162B SER* 1.3 75.9 - - - +
164B ALA* 1.3 62.3 + - - +
166B LEU* 3.1 14.9 + - - +
167B VAL* 3.2 18.9 + - - +
175B ALA* 3.8 19.0 - - + +
176B ALA 5.6 0.7 - - - -
177B THR* 6.0 1.1 - - + -
182B CYS* 4.2 1.3 - - - -
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Residues in contact with ALA 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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160B GLU 3.1 6.4 + - - +
161B ALA 3.2 10.1 + - - +
163B CYS* 1.3 77.7 - - - +
165B ALA* 1.3 62.6 + - - +
167B VAL* 3.1 4.2 + - - +
168B LYS* 3.0 28.8 + - - +
182B CYS* 3.6 13.6 - - - +
185B PHE* 4.1 11.2 - - + +
186B GLY 3.7 5.1 - - - +
187B SER* 3.5 37.2 - - - +
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Residues in contact with ALA 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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161B ALA 2.9 13.6 + - - +
162B SER* 3.3 10.3 - - - +
163B CYS 3.2 0.2 - - - -
164B ALA* 1.3 77.1 - - - +
166B LEU* 1.3 59.9 + - - +
168B LYS* 3.5 17.0 + - + +
169B ALA* 3.1 24.3 + - - +
288B VAL* 3.8 28.7 - - + -
289B LEU 4.5 2.0 - - - +
291B PRO* 3.6 18.7 - - + +
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Residues in contact with LEU 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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32B ALA* 4.1 19.7 - - + -
82B VAL* 5.4 2.2 - - + -
84B VAL* 4.2 8.7 - - + -
153B LEU* 3.7 24.2 - - + -
162B SER 3.0 17.7 + - - +
163B CYS 3.1 6.7 + - - +
165B ALA* 1.3 74.3 - - - +
167B VAL* 1.3 65.1 + - - +
169B ALA 3.6 0.9 + - - -
170B GLY 3.2 2.4 + - - -
171B LYS* 3.1 43.1 + - + -
172B VAL* 3.5 20.9 + - + -
289B LEU* 4.2 12.1 - - + -
291B PRO* 3.8 27.4 - - + -
294B VAL* 4.2 12.1 - - + -
296B LEU* 5.9 2.2 - - + -
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Residues in contact with VAL 167 (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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163B CYS 3.3 14.8 - - - +
164B ALA 3.1 6.4 + - - +
166B LEU* 1.3 75.0 - - - +
168B LYS* 1.3 65.6 + - - +
170B GLY* 2.9 15.8 + - - -
172B VAL* 3.9 14.9 - - + +
173B TYR 3.7 18.2 - - - +
174B ALA* 4.0 24.5 - - - -
175B ALA* 4.0 1.8 - - + +
187B SER* 3.7 14.4 - - - +
188B PRO* 3.5 32.8 - - + +
189B VAL* 3.9 6.7 - - + +
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Residues in contact with LYS 168 (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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161B ALA 5.7 0.6 + - - -
164B ALA* 3.0 19.6 + - - +
165B ALA* 3.6 16.0 - - + +
167B VAL* 1.3 77.2 - - - +
169B ALA* 1.3 60.0 + - + +
170B GLY* 3.4 0.7 + - - -
185B PHE 2.9 23.0 + - - -
186B GLY* 2.9 31.1 - - - +
188B PRO* 4.1 12.3 - - + +
284B LEU 5.8 1.6 + - - -
286B PRO* 5.3 8.3 - - - +
288B VAL* 6.2 1.2 - - - +
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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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165B ALA 3.1 15.4 + - - +
166B LEU 4.1 3.1 - - - +
167B VAL 3.2 0.4 - - - -
168B LYS* 1.3 77.7 - - - +
170B GLY* 1.3 58.0 + - - +
171B LYS* 3.3 20.0 + - + -
291B PRO* 3.6 25.8 - - + -
292B GLU* 3.9 14.9 - - + +
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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