Contacts of the helix formed by residues 226 - 237 (chain A) 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 ASN 226 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A GLN 3.5 16.1 + - - +
123A ILE* 2.9 27.4 + - - -
124A MET 3.7 1.8 + - - -
125A SER* 3.7 30.5 + - - -
128A GLY* 4.6 2.0 - - - -
224A VAL 3.4 1.0 + - - -
225A VAL* 1.3 69.3 - - - +
227A TRP* 1.3 62.2 + - - +
228A SER* 3.2 20.5 + - - -
229A GLU* 3.3 15.8 + - - +
230A ILE* 3.1 25.3 + - - +
232A ARG* 5.2 2.6 - - - +
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Residues in contact with TRP 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY* 5.5 0.4 - - - -
129A GLY 3.5 22.4 + - - -
130A GLY 3.0 18.8 + - - -
131A GLN 3.6 12.6 - - - -
132A PRO* 3.5 35.4 - - + -
133A THR* 4.1 19.5 - - + +
136A ILE* 4.2 19.1 - - + -
140A ILE* 4.6 2.0 - - + -
147A PHE* 3.8 16.4 - + - -
150A PHE* 4.5 5.6 - + - -
197A MET* 4.2 9.0 - - - -
222A TRP* 4.1 21.9 + + - -
225A VAL* 3.4 22.5 + - + +
226A ASN* 1.3 72.5 + - - +
228A SER* 1.3 61.6 + - - +
230A ILE* 3.3 34.2 + - + +
231A ASN* 3.0 29.4 + - - +
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 5.3 1.6 + - - -
226A ASN* 3.2 11.1 + - - -
227A TRP* 1.3 78.3 - - - +
229A GLU* 1.3 62.8 + - - +
231A ASN* 3.3 16.8 + - - +
232A ARG* 3.4 37.1 + - - +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.6 21.7 - - - +
122A GLN* 3.5 42.4 - - + +
123A ILE* 4.5 1.8 - - + -
226A ASN* 3.3 27.4 + - + +
228A SER* 1.3 76.4 - - - +
230A ILE* 1.3 66.8 + - - +
232A ARG* 2.7 43.8 + - - +
233A ARG* 3.0 41.3 + - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123A ILE* 4.0 23.3 - - + -
136A ILE* 4.1 11.2 - - + -
196A ILE* 3.6 20.8 - - + +
197A MET* 3.7 27.8 - - + -
225A VAL* 3.3 33.9 - - + -
226A ASN 3.1 10.9 + - - +
227A TRP* 3.7 26.7 - - + +
228A SER 3.3 0.4 - - - -
229A GLU* 1.3 76.2 - - - +
231A ASN* 1.3 56.9 + - - +
233A ARG* 3.3 8.4 + - - +
234A THR* 2.8 35.4 + - - +
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Residues in contact with ASN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR* 2.8 32.3 + - - -
134A GLY* 4.3 2.0 - - - -
135A ASP* 3.6 12.3 + - - +
136A ILE* 2.9 34.9 + - - +
227A TRP 3.0 19.3 + - - -
228A SER* 3.5 11.5 - - - +
229A GLU 3.1 0.4 - - - -
230A ILE* 1.3 74.9 - - - +
232A ARG* 1.3 64.4 + - + +
234A THR* 3.3 4.9 + - - -
235A GLN* 3.0 39.1 + - - +
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Residues in contact with ARG 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 3.3 22.0 - - + +
226A ASN* 5.2 2.6 - - - +
228A SER* 3.5 27.5 + - - +
229A GLU* 2.7 48.4 + - - +
231A ASN* 1.3 76.3 - - + +
233A ARG* 1.3 58.3 + - - +
235A GLN* 3.3 14.8 + - - +
236A ALA* 3.0 27.7 + - - +
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Residues in contact with ARG 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 2.5 30.5 + - - +
27A GLY 3.4 13.9 + - - -
28A PHE* 5.1 2.6 - - - +
29A ILE* 4.0 18.1 - - + +
119A ILE* 3.7 24.6 + - - +
122A GLN* 5.3 3.8 + - - +
123A ILE* 3.8 17.7 - - - +
194A TYR* 3.6 23.1 + - + +
195A PRO 2.7 29.5 + - - -
196A ILE* 3.2 24.8 + - + +
229A GLU* 3.0 26.6 + - - +
230A ILE* 3.6 7.4 - - - +
232A ARG* 1.3 75.0 - - - +
234A THR* 1.3 58.5 + - - +
236A ALA* 3.4 1.2 + - - +
237A SER* 2.9 29.7 + - - -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASP* 5.3 6.3 - - + -
136A ILE* 3.3 40.0 - - + +
139A GLU* 3.8 11.0 - - - +
171A ARG* 3.4 24.5 + - - +
177A LEU* 5.3 0.4 - - + -
196A ILE* 3.7 11.8 - - + +
230A ILE 2.8 23.9 + - - -
231A ASN* 3.6 9.2 - - - -
233A ARG* 1.3 75.2 - - - +
235A GLN* 1.3 61.2 + - + +
237A SER* 3.0 23.2 + - - -
238A ARG 3.4 4.0 + - - -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A ASP* 4.1 27.0 + - + +
231A ASN* 3.0 28.7 + - - +
232A ARG* 3.5 12.9 - - - +
234A THR* 1.3 75.4 - - - +
236A ALA* 1.3 65.0 + - - +
237A SER 3.2 0.5 + - - -
238A ARG 3.2 9.2 + - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER 6.1 0.2 - - - +
29A ILE* 3.8 25.4 - - + +
194A TYR* 3.8 20.9 - - + +
232A ARG 3.0 16.2 + - - +
233A ARG* 3.4 5.6 + - - +
235A GLN* 1.3 75.4 - - - +
237A SER* 1.3 62.2 + - - +
238A ARG 3.3 0.9 + - - -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ARG* 2.7 55.0 + - - +
194A TYR* 3.8 20.8 - - - +
196A ILE* 3.5 15.9 - - - +
233A ARG 2.9 14.7 + - - -
234A THR 3.0 16.2 - - - -
236A ALA* 1.3 77.4 - - - +
238A ARG 1.3 44.5 + - - +
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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