Contacts of the helix formed by residues 1168 - 1177 (chain M) in PDB entry 2X4Y
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 ASN1168 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1197E GLN* 4.0 12.0 + - - +
1200E SER* 4.9 13.0 + - - -
1205E GLU* 5.3 4.2 - - - +
1164M PRO 5.7 0.4 + - - -
1167M VAL* 1.3 86.7 - - + +
1169M GLN* 1.3 59.7 + - - +
1170M ASP* 2.9 16.8 + - - +
1171M LEU* 2.8 42.3 - - + +
1172M ASP* 3.0 30.7 + - - +
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Residues in contact with GLN1169 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167M VAL 4.3 0.2 - - - -
1168M ASN* 1.3 71.6 - - - +
1170M ASP* 1.3 62.9 + - - +
1172M ASP* 3.2 9.4 + - + +
1173M LYS* 2.8 63.7 + - + +
1192M TYR* 5.6 2.9 - - - +
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Residues in contact with ASP1170 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1193E HIS* 3.0 49.7 + - - +
1196E LEU* 3.5 34.0 - - + +
1197E GLN* 3.7 8.3 - - + +
1200E SER* 4.8 5.5 + - - -
1168M ASN* 2.9 9.1 + - - +
1169M GLN* 1.3 79.3 - - - +
1171M LEU* 1.3 64.5 + - - +
1173M LYS* 3.4 3.5 + - - +
1174M GLU* 2.9 24.3 + - - +
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Residues in contact with LEU1171 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1197E GLN* 3.6 29.0 - - - +
1090M TRP* 3.8 4.7 - - + -
1163M VAL* 3.8 33.7 - - + -
1164M PRO 4.0 5.4 - - - +
1168M ASN* 2.8 32.2 - - + +
1170M ASP* 1.3 73.5 - - - +
1172M ASP* 1.3 78.2 + - - +
1174M GLU* 3.1 7.2 + - - +
1175M LYS* 2.9 46.5 + - + +
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Residues in contact with ASP1172 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M TRP* 2.9 28.1 + - - +
1164M PRO 4.4 0.2 - - - +
1165M LEU* 3.8 0.5 - - - -
1166M GLY* 3.0 34.5 + - - -
1167M VAL 4.5 0.3 + - - -
1168M ASN 3.0 19.0 + - - +
1169M GLN* 3.2 10.6 + - + +
1171M LEU* 1.3 82.0 - - - +
1173M LYS* 1.3 57.9 + - + +
1175M LYS 3.3 0.9 + - - -
1176M MET* 3.0 34.3 + - + +
1192M TYR* 2.8 40.9 + - + +
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Residues in contact with LYS1173 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1193E HIS* 3.5 39.1 - - + +
1169M GLN* 2.8 57.4 + - + +
1170M ASP* 3.9 4.1 + - - +
1172M ASP* 1.3 76.7 - - + +
1174M GLU* 1.3 64.5 + - - +
1176M MET* 3.3 26.7 + - + +
1177M LEU* 3.4 19.7 + - + +
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Residues in contact with GLU1174 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190E ILE* 3.9 26.6 - - + +
1193E HIS* 4.2 11.1 - - + +
1194E ARG* 3.3 34.8 + - + +
1197E GLN* 2.8 27.3 + - - +
1170M ASP 2.9 13.9 + - - +
1171M LEU* 3.1 10.7 + - - +
1173M LYS* 1.3 76.1 - - - +
1175M LYS* 1.3 69.1 + - + +
1177M LEU* 3.2 14.1 + - - +
1178M GLU* 3.6 8.3 + - - +
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Residues in contact with LYS1175 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M TRP* 3.5 52.3 - - + +
1097M PRO* 5.6 0.2 - - - +
1098M SER* 3.9 25.3 + - - +
1163M VAL* 3.7 37.4 - - - +
1171M LEU* 2.9 29.2 + - + +
1172M ASP 3.7 0.7 - - - +
1174M GLU* 1.3 83.9 + - + +
1176M MET* 1.3 63.6 + - - +
1177M LEU 3.1 1.2 + - - -
1178M GLU* 3.1 27.4 + - - +
1188M VAL* 4.7 3.3 - - - +
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Residues in contact with MET1176 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090M TRP* 3.7 19.1 - - + -
1172M ASP* 3.0 27.7 + - + +
1173M LYS* 3.7 21.3 - - + +
1174M GLU 3.3 0.4 - - - -
1175M LYS* 1.3 76.4 - - - +
1177M LEU* 1.3 64.5 + - + +
1178M GLU 3.4 0.6 + - - -
1179M GLY 4.8 0.5 + - - -
1185M ARG* 4.1 21.3 - - - +
1188M VAL* 4.2 15.7 - - + +
1189M GLN* 4.2 29.1 + - + +
1192M TYR* 3.7 42.8 - - + -
1193M HIS* 5.0 5.8 - - + -
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Residues in contact with LEU1177 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1186E LYS* 2.8 43.7 + - + +
1189E GLN* 3.5 47.6 - - + +
1190E ILE* 3.7 28.2 - - + +
1193E HIS* 4.5 7.6 - - + +
1173M LYS* 3.5 15.0 - - + +
1174M GLU 3.2 3.5 + - - +
1175M LYS 3.0 1.4 - - - -
1176M MET* 1.3 82.9 - - + +
1178M GLU* 1.3 57.3 + - - +
1179M GLY 3.4 2.4 + - - -
1185M ARG* 4.1 11.7 - - - +
1189M GLN* 6.0 2.9 - - - +
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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