Contacts of the helix formed by residues 1191 - 1196 (chain D) in PDB entry 1W1W
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 LYS1191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1161C ALA 5.4 1.6 - - - -
1190C LEU* 5.3 4.4 - - - +
1191C LYS* 4.7 21.8 - - - +
1160D ASP* 3.3 43.3 + - - +
1161D ALA* 3.6 16.1 + - - +
1163D LEU 3.5 18.2 + - - -
1168D VAL* 3.8 19.3 - - + +
1189D SER* 2.8 7.4 + - - +
1190D LEU* 1.3 83.6 - - + +
1192D ASN* 1.3 57.3 + - - +
1193D THR* 4.3 5.8 - - - +
1194D MET* 2.7 33.1 + - + +
1195D PHE* 3.2 15.2 + - - -
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Residues in contact with ASN1192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1190D LEU 3.9 3.4 + - - +
1191D LYS* 1.3 70.3 - - - +
1193D THR* 1.3 59.6 + - - +
1195D PHE* 3.5 29.4 - - - -
1196D GLU* 2.8 48.2 + - - +
522H ARG* 4.1 5.9 + - - +
525H SER* 4.7 1.0 + - - -
526H ARG* 3.3 64.0 + - - +
529H PHE* 5.6 3.8 - - - +
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Residues in contact with THR1193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1165D ILE* 4.0 22.6 - - + +
1168D VAL* 3.6 25.6 - - + +
1169D GLN* 3.9 34.1 - - + +
1172D ALA* 4.2 4.0 - - - +
1191D LYS* 4.7 5.5 - - - +
1192D ASN* 1.3 78.1 + - - +
1194D MET* 1.3 60.7 + - - +
1196D GLU* 4.2 12.0 + - - +
1197D LYS* 4.0 20.8 - - - +
522H ARG* 5.6 4.8 + - - +
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Residues in contact with MET1194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D PHE* 3.8 26.3 - - + -
30D SER* 4.3 3.8 - - - +
1159D VAL* 6.2 1.6 - - - -
1160D ASP* 3.0 25.1 - - + +
1168D VAL* 3.8 17.6 - - + +
1171D ILE* 4.9 7.2 - - + -
1172D ALA* 4.1 26.9 - - - +
1175D ILE* 4.5 8.3 - - + -
1187D VAL* 3.4 34.5 - - + -
1189D SER* 3.3 11.7 - - - +
1191D LYS* 2.7 11.7 + - + +
1193D THR* 1.3 78.1 - - - +
1195D PHE* 1.3 65.4 + - - +
1196D GLU 3.2 2.7 + - - -
1197D LYS* 3.3 16.6 + - - +
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Residues in contact with PHE1195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D SER* 3.3 27.3 + - - -
32D ILE* 3.2 37.5 - - + -
1189D SER* 3.9 10.5 - - - -
1190D LEU* 4.1 12.3 - - - -
1191D LYS 3.2 25.8 + - - -
1192D ASN* 3.5 38.8 - - - -
1194D MET* 1.3 74.7 - - + +
1196D GLU* 1.3 69.1 + - - +
1197D LYS 3.0 2.2 - - - -
1198D SER* 2.7 26.6 + - - -
1201D LEU* 3.7 3.5 - - + +
1220D LEU* 3.5 8.7 - - - +
525H SER* 3.7 30.3 - - - -
529H PHE* 4.7 13.5 - + + -
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Residues in contact with GLU1196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192D ASN* 2.8 45.2 + - + +
1193D THR* 4.2 11.1 + - - +
1195D PHE* 1.3 74.1 - - - +
1197D LYS* 1.3 72.6 + - + +
1198D SER 3.3 3.3 + - - -
1220D LEU* 3.7 5.2 - - - +
521H LYS* 3.4 26.0 - - + +
522H ARG* 2.8 69.0 + - + +
525H SER* 3.9 14.6 - - - +
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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