Contacts of the helix formed by residues 132 - 143 (chain B) in PDB entry 3GV5
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 LEU 132 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 2.8 26.9 + - + +
31B VAL* 3.8 32.3 - - + -
130B VAL* 4.0 8.7 - - + +
131B ASP* 1.3 70.7 - - - +
133B THR* 1.3 59.1 + - - +
134B GLU 3.3 2.9 - - - -
135B MSE 3.2 15.4 + - + -
136B VAL* 2.9 32.9 + - + +
176B GLY* 3.7 34.8 - - - +
179B ILE* 3.9 19.3 - - + -
180B ALA 4.7 1.3 - - - +
183B MSE 3.6 30.7 - - + -
199B VAL* 5.0 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ARG* 3.5 18.7 - - + +
29B VAL* 3.3 32.2 + - - +
131B ASP* 2.3 40.1 + - - +
132B LEU* 1.3 77.7 - - - +
134B GLU* 1.3 62.2 + - - +
136B VAL* 3.9 6.1 - - - +
137B GLU* 3.1 25.3 + - - +
172B ARG* 6.1 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER* 6.2 0.2 - - - +
131B ASP* 4.7 4.6 + - - +
132B LEU 5.1 0.4 - - - -
133B THR* 1.3 76.4 + - - +
135B MSE 1.3 64.7 + - - +
137B GLU* 2.9 32.4 + - - +
138B LYS* 2.7 52.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 3.2 53.4 - - + +
117B SER* 4.6 5.8 - - - +
131B ASP 5.6 0.4 - - - +
132B LEU* 3.2 22.4 + - + +
134B GLU* 1.3 82.8 + - - +
136B VAL* 1.3 60.3 + - - +
138B LYS* 3.4 14.9 + - + +
139B ARG* 3.0 39.6 + - + +
179B ILE* 3.6 39.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B VAL* 4.2 12.8 - - + -
132B LEU* 2.9 23.9 + - + +
133B THR* 3.9 6.5 - - - +
135B MSE 1.3 72.3 - - - +
137B GLU* 1.3 58.7 + - - +
139B ARG* 3.2 4.0 + - - +
140B LEU* 3.0 38.7 + - + +
172B ARG* 3.6 38.8 - - + +
175B VAL* 3.7 17.3 - - + -
176B GLY* 3.7 28.0 - - - +
179B ILE* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 3.1 17.1 + - - +
134B GLU* 2.9 34.2 - - - +
136B VAL* 1.3 77.2 - - - +
138B LYS* 1.3 65.5 + - - +
140B LEU* 3.6 8.8 + - - +
141B GLN* 3.2 47.8 + - - +
172B ARG* 6.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLU* 2.7 42.6 + - - +
135B MSE 3.6 16.5 - - + +
137B GLU* 1.3 79.0 - - - +
139B ARG* 1.3 62.7 - - + +
141B GLN* 3.3 16.3 + - - +
142B GLN* 3.2 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B PHE* 5.5 1.0 - - - -
135B MSE 3.0 34.1 + - + +
136B VAL 3.2 7.2 + - - +
138B LYS* 1.3 75.2 - - + +
140B LEU* 1.3 58.2 + - - +
142B GLN* 3.4 17.1 + - - +
143B LEU* 3.0 40.2 + - + +
175B VAL* 3.9 24.0 + - + -
178B GLN* 4.9 9.5 + - - +
179B ILE* 3.5 27.2 - - - +
182B GLU* 2.7 44.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B VAL* 3.0 28.0 + - + +
137B GLU* 3.9 7.6 - - - +
138B LYS 3.3 0.2 - - - -
139B ARG* 1.3 72.6 - - - +
141B GLN* 1.3 65.4 + - - +
143B LEU* 3.4 37.4 + - + +
148B LEU* 4.9 3.1 - - + -
168B VAL* 5.6 3.6 - - + -
171B ILE* 3.4 30.5 - - + -
172B ARG* 3.8 34.5 - - + +
175B VAL* 4.0 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU* 3.2 43.8 + - - +
138B LYS* 3.5 16.4 - - - +
140B LEU* 1.3 77.0 - - + +
142B GLN* 1.3 62.2 + - + +
143B LEU 3.5 5.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LYS* 3.2 41.9 + - - +
139B ARG* 3.4 18.9 + - - +
141B GLN* 1.3 74.8 - - + +
143B LEU* 1.3 66.0 + - + +
144B GLN* 3.7 4.9 + - - +
147B GLU* 5.0 0.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B ARG* 3.0 30.7 + - + +
140B LEU* 3.4 31.3 - - + +
141B GLN 3.3 7.5 - - - +
142B GLN* 1.3 80.6 - - + +
144B GLN* 1.3 68.2 + - - +
147B GLU* 4.1 14.8 - - + +
148B LEU* 3.8 31.2 - - + -
151B VAL* 3.9 18.4 - - + -
175B VAL* 5.4 5.4 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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