Contacts of the helix formed by residues 133 - 145 (chain B) in PDB entry 1GV3
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 133 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN 4.1 7.2 - - - +
132B PRO* 1.3 78.1 - - - +
134B GLY* 1.3 65.0 + - - +
136B ILE* 3.7 0.9 - - - +
137B ALA* 3.6 12.1 + - - -
227B TRP* 4.4 13.1 + - + +
228B SER* 5.3 1.9 + - - -
231B ASN* 2.7 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B THR* 1.3 76.4 - - - +
135B ASP* 1.3 65.3 + - - +
137B ALA* 3.3 16.1 + - - +
138B GLN* 3.5 14.5 + - - +
231B ASN* 4.2 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY* 1.3 71.4 - - - -
136B ILE* 1.3 62.9 + - - +
138B GLN* 3.2 17.0 + - - +
139B GLU* 3.1 25.5 + - - +
231B ASN* 3.4 11.8 + - - +
234B THR* 4.9 10.5 - - + -
235B GLN* 4.8 23.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 4.2 4.5 - - + -
133B THR 3.7 7.9 - - - +
135B ASP* 1.3 78.8 - - - +
137B ALA* 1.3 59.1 + - - +
139B GLU* 4.2 4.3 - - - -
140B ILE* 2.8 44.8 + - + +
169B LEU* 3.9 25.4 - - + -
177B LEU* 5.1 5.8 - - + -
196B ILE* 4.1 4.3 - - + -
227B TRP* 4.2 20.9 - - + -
230B ILE* 3.5 22.2 - - + -
231B ASN* 3.1 21.5 + - - +
234B THR* 3.3 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 3.6 40.2 - - + +
133B THR* 3.6 9.6 + - - +
134B GLY 3.3 11.8 + - - +
135B ASP 3.2 0.6 - - - -
136B ILE* 1.3 81.8 - - - +
138B GLN* 1.3 58.6 + - - +
140B ILE* 3.8 2.4 - - - +
141B ASN* 3.1 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLY 3.5 12.0 + - - +
135B ASP* 3.2 22.9 + - - +
137B ALA* 1.3 77.4 - - - +
139B GLU* 1.3 64.9 + - + +
141B ASN* 3.4 9.9 + - - +
142B GLN* 3.1 36.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ASP* 3.1 17.8 + - - +
136B ILE* 3.8 5.2 - - - +
138B GLN* 1.3 76.1 - - + +
140B ILE* 1.3 65.7 + - - +
142B GLN* 3.4 13.2 + - - +
143B THR* 2.9 34.3 + - - +
171B ARG* 2.7 45.4 + - - -
175B GLY 4.7 0.5 - - - +
177B LEU* 3.4 23.0 + - + +
234B THR* 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PRO* 4.6 9.0 - - + -
136B ILE* 2.8 45.5 + - + +
137B ALA* 3.8 4.3 - - - +
139B GLU* 1.3 77.0 - - - +
141B ASN* 1.3 59.3 + - - +
144B PHE* 2.9 38.6 + - + +
145B GLY 3.7 0.5 + - - -
146B SER 3.9 8.5 - - - +
147B PHE* 4.1 12.1 - - + -
150B PHE* 3.7 56.1 - - + -
169B LEU* 4.8 2.2 - - + -
177B LEU* 4.6 8.5 - - + -
227B TRP* 4.5 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B GLN* 5.8 1.2 + - - -
137B ALA* 3.1 23.5 + - - +
138B GLN* 3.7 9.4 - - - +
139B GLU 3.3 0.4 - - - -
140B ILE* 1.3 78.0 - - - +
142B GLN* 1.3 58.4 + - + +
145B GLY* 3.0 36.4 + - - +
146B SER* 3.5 18.7 - - - -
147B PHE* 3.6 10.2 + - - +
----------------------------------------------------------
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 GLN* 3.1 27.5 + - + +
139B GLU* 3.8 13.4 - - - +
140B ILE 3.3 0.2 - - - -
141B ASN* 1.3 79.1 - - + +
143B THR* 1.3 65.9 + - - +
145B GLY* 4.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLU* 2.9 22.1 + - - +
142B GLN* 1.3 81.4 - - - +
144B PHE* 1.3 88.5 + - + +
145B GLY 3.9 0.2 + - - -
176B GLN* 6.2 0.7 - - + -
177B LEU* 4.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 2.9 24.5 + - + +
143B THR* 1.3 98.1 - - + +
145B GLY* 1.3 57.1 + - - +
146B SER 3.4 3.4 - - - +
149B GLU* 3.5 22.9 - - - +
150B PHE* 3.8 44.9 - + + +
153B GLN* 3.7 32.4 + - - +
169B LEU* 4.1 12.6 - - + -
177B LEU* 4.2 23.3 - - + -
178B GLN* 5.1 1.1 - - - -
179B VAL* 3.9 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE 3.7 0.2 + - - -
141B ASN* 3.0 26.4 + - - +
142B GLN 4.4 1.7 + - - -
143B THR 3.6 1.8 + - - -
144B PHE* 1.3 76.8 - - - +
146B SER* 1.3 62.8 + - - +
149B GLU* 4.0 9.6 - - - -
----------------------------------------------------------
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