Contacts of the helix formed by residues 1168 - 1177 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1164K PRO 5.5 1.9 + - - +
1166K GLY 5.3 0.2 - - - -
1167K VAL* 1.3 85.2 - - + +
1169K GLN* 1.3 58.7 + - - +
1170K ASP* 3.1 13.3 + - - +
1171K LEU* 3.1 37.8 + - + +
1172K ASP* 3.0 30.2 + - - -
1197M GLN* 4.1 12.9 + - - +
1200M SER* 4.5 16.4 + - - -
1205M GLU* 4.5 15.2 + - - +
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Residues in contact with GLN1169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1167K VAL 4.2 0.6 - - - -
1168K ASN* 1.3 72.9 + - - +
1170K ASP* 1.3 79.1 + - - +
1172K ASP* 3.4 9.3 + - - +
1173K LYS* 3.0 59.2 + - - +
1192K TYR* 5.7 0.7 - - - -
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Residues in contact with ASP1170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1168K ASN* 3.1 5.5 + - - +
1169K GLN* 1.3 92.9 - - - +
1171K LEU* 1.3 60.8 + - - +
1173K LYS* 3.4 0.9 + - - +
1174K GLU* 2.9 25.1 + - - +
1193M HIS* 3.0 51.4 + - - +
1196M LEU* 3.5 38.3 - - + +
1197M GLN* 3.5 12.0 + - + -
1199M ARG* 5.8 0.3 + - - -
1200M SER* 5.9 1.2 - - - -
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Residues in contact with LEU1171 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090K TRP* 3.6 29.6 - - + +
1163K VAL* 3.6 29.4 - - + -
1164K PRO 4.2 4.5 - - - +
1168K ASN* 3.1 31.8 + - + +
1170K ASP* 1.3 77.7 - - - +
1172K ASP* 1.3 67.6 + - - +
1174K GLU* 3.2 3.5 + - - +
1175K LYS* 2.9 45.6 + - + +
1197M GLN* 3.5 26.1 - - - +
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Residues in contact with ASP1172 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090K TRP* 2.9 29.2 + - - +
1164K PRO 4.4 0.7 - - - +
1165K LEU* 3.9 0.5 - - - -
1166K GLY* 3.1 30.8 + - - -
1167K VAL 4.5 0.5 + - - -
1168K ASN 3.0 19.7 + - - +
1169K GLN* 3.7 10.6 - - - +
1171K LEU* 1.3 79.4 - - - +
1173K LYS* 1.3 57.7 + - + +
1175K LYS 3.3 1.0 + - - -
1176K MET* 2.9 33.1 + - + +
1192K TYR* 2.7 42.8 + - + +
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Residues in contact with LYS1173 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1169K GLN* 3.0 47.4 + - - +
1170K ASP* 3.9 1.5 + - - +
1172K ASP* 1.3 73.9 - - + +
1174K GLU* 1.3 68.8 + - - +
1176K MET* 3.3 23.9 + - + +
1177K LEU* 3.5 20.0 + - + +
1193M HIS* 3.4 41.6 - - + +
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Residues in contact with GLU1174 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1170K ASP 2.9 17.8 + - - +
1171K LEU* 3.5 5.5 - - - +
1173K LYS* 1.3 78.0 - - - +
1175K LYS* 1.3 74.4 + - - +
1177K LEU* 3.1 17.7 + - - +
1178K GLU* 3.6 8.3 + - - +
1190M ILE* 4.0 20.9 - - + +
1193M HIS* 4.1 11.6 - - + +
1194M ARG* 3.3 35.4 + - + +
1197M GLN* 2.7 32.0 + - - +
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Residues in contact with LYS1175 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090K TRP* 3.5 51.4 - - + -
1098K SER* 3.5 34.5 - - - +
1163K VAL* 4.2 18.5 - - - +
1171K LEU* 2.9 41.4 + - + +
1174K GLU* 1.3 89.1 + - + +
1176K MET* 1.3 62.1 + - - +
1177K LEU 3.1 0.7 + - - -
1178K GLU* 3.2 26.1 + - - +
1179K GLY 4.9 0.3 + - - -
1188K VAL* 4.5 3.6 - - - +
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Residues in contact with MET1176 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1090K TRP* 3.6 17.9 - - + -
1172K ASP* 2.9 25.7 + - + +
1173K LYS* 3.3 18.6 + - + +
1174K GLU 3.2 0.8 - - - -
1175K LYS* 1.3 77.8 - - - +
1177K LEU* 1.3 63.4 + - + +
1178K GLU 3.7 0.3 + - - -
1179K GLY 4.6 0.5 + - - -
1185K ARG* 4.0 21.3 - - - +
1188K VAL* 4.0 19.4 - - + +
1189K GLN* 4.2 26.4 + - + +
1192K TYR* 3.8 44.4 - - + -
1193K HIS* 5.1 4.5 - - + +
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Residues in contact with LEU1177 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1173K LYS* 3.5 15.7 - - + +
1174K GLU 3.1 3.5 + - - +
1175K LYS 3.0 1.0 - - - -
1176K MET* 1.3 81.3 - - + +
1178K GLU* 1.3 59.1 + - - +
1179K GLY 3.2 3.8 + - - +
1185K ARG* 4.1 10.8 - - - +
1189K GLN* 6.2 1.8 - - - +
1186M LYS* 2.9 45.5 + - + +
1189M GLN* 3.6 46.4 - - + +
1190M ILE* 3.6 32.5 - - + +
1193M HIS* 4.5 7.0 - - + +
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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