Contacts of the helix formed by residues 1117 - 1127 (chain F) in PDB entry 5YW9
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 PRO1117 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1115F THR 3.6 6.9 - - - +
1116F THR* 1.3 98.6 - - + +
1118F LEU* 1.3 65.6 + - - +
1119F GLY* 3.3 5.4 - - - +
1120F SER* 3.3 20.7 + - - +
1121F ILE* 3.7 6.1 - - - +
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Residues in contact with LEU1118 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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500F ASN* 4.1 11.7 - - + +
503F LEU* 2.4 58.1 - - + +
504F ARG* 3.0 56.3 - - + +
506F MET* 5.8 2.6 - - + +
1116F THR 3.7 1.2 + - - -
1117F PRO* 1.3 74.4 - - - +
1119F GLY* 1.3 64.6 + - - +
1120F SER 3.3 0.2 + - - -
1121F ILE* 3.4 3.2 + - + +
1122F LEU* 2.9 31.2 + - + +
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Residues in contact with GLY1119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1117F PRO* 3.3 5.2 - - - +
1118F LEU* 1.3 78.6 - - - +
1120F SER* 1.3 56.9 + - - +
1122F LEU* 4.3 2.6 - - - +
1123F ASN* 2.8 37.1 + - - +
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Residues in contact with SER1120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116F THR* 3.2 27.2 - - - +
1117F PRO* 3.3 10.5 + - - +
1119F GLY* 1.3 72.8 - - - +
1121F ILE* 1.3 71.1 + - - +
1123F ASN* 3.9 4.8 - - - +
1124F ARG* 2.8 49.6 + - - +
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Residues in contact with ILE1121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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503F LEU* 2.6 51.2 - - + +
506F MET* 5.9 0.9 - - + -
1105F ILE* 4.2 20.4 - - + -
1112F PHE* 4.4 15.3 - - + -
1113F PHE* 4.2 17.9 - - + +
1116F THR* 3.6 38.8 - - + +
1117F PRO 3.7 6.7 - - - +
1118F LEU* 3.4 5.5 + - - +
1120F SER* 1.3 78.0 + - - +
1122F LEU* 1.3 59.1 + - - +
1124F ARG* 3.9 12.5 + - - +
1125F PHE* 3.9 16.3 + - + -
1318F LEU* 4.6 8.8 - - + +
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Residues in contact with LEU1122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F LEU* 4.5 3.3 - - + +
499F THR* 4.6 13.1 - - + +
500F ASN* 5.4 6.5 - - + -
503F LEU* 3.2 12.7 - - + +
1118F LEU* 2.9 26.6 + - + +
1119F GLY* 4.3 2.0 - - - +
1121F ILE* 1.3 76.3 - - - +
1123F ASN* 1.3 60.5 + - - +
1125F PHE* 3.3 7.0 + - - +
1126F SER* 3.0 27.7 + - - -
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Residues in contact with ASN1123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1119F GLY 2.8 25.7 + - - +
1120F SER* 3.9 6.0 - - - +
1121F ILE 3.4 0.2 - - - -
1122F LEU* 1.3 71.9 - - - +
1124F ARG* 1.3 65.9 + - + +
1126F SER* 2.6 24.1 + - - -
1127F SER* 2.9 19.8 + - - -
1128F ASP* 4.3 0.8 - - - +
1314F ARG* 5.6 6.2 - - - +
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Residues in contact with ARG1124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1101F LEU* 5.2 0.9 - - + -
1116F THR* 5.5 1.0 - - - +
1120F SER* 2.8 52.7 + - - +
1121F ILE* 3.6 8.9 - - - +
1122F LEU 3.3 0.4 - - - -
1123F ASN* 1.3 75.2 - - + +
1125F PHE* 1.3 61.5 + - + +
1128F ASP* 2.9 53.1 + - - +
1129F CYS* 3.1 4.0 - - - -
1314F ARG* 3.5 38.3 + - - +
1315F ILE* 3.8 12.8 - - + -
1317F ALA* 5.6 3.8 - - - +
1318F LEU* 3.0 42.0 - - + +
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Residues in contact with PHE1125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495F ARG* 2.8 33.8 + - - +
496F LEU* 4.7 3.1 - - + -
499F THR* 4.5 22.4 - - + +
522F VAL* 6.2 1.3 - - + -
1098F HIS* 4.0 21.5 - + - -
1101F LEU* 2.8 44.2 - - + -
1102F LEU* 4.0 24.5 - - + -
1105F ILE* 3.5 26.5 - - + -
1121F ILE* 3.9 13.9 - - + -
1122F LEU 3.3 6.8 + - - +
1123F ASN 3.3 0.4 - - - -
1124F ARG* 1.3 79.7 - - + +
1126F SER* 1.3 60.3 + - - +
1129F CYS* 2.5 32.2 - - - +
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Residues in contact with SER1126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496F LEU* 3.0 40.0 - - - +
1122F LEU* 3.0 14.0 + - - -
1123F ASN* 2.6 33.4 + - - -
1125F PHE* 1.3 77.4 - - - +
1127F SER* 1.3 53.9 + - - +
1130F ASN* 2.3 34.2 + - - -
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Residues in contact with SER1127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1123F ASN* 2.9 22.2 + - - -
1126F SER* 1.3 82.3 + - - +
1128F ASP* 1.3 73.3 + - - +
1129F CYS 3.0 1.8 - - - -
1130F ASN* 2.5 7.1 + - - -
1131F THR* 2.5 38.4 + - - +
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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