Contacts of the strand formed by residues 1178 - 1187 (chain C) in PDB entry 5YS0
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 THR1178 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1068C ASN* 3.4 7.5 - - - -
1069C ILE* 3.0 35.3 + - + +
1071C VAL 2.8 22.9 + - - -
1073C LEU* 3.1 26.6 - - + -
1076C VAL* 3.4 18.6 - - + +
1170C TYR* 3.8 36.8 - - + -
1171C SER 3.6 3.4 - - - -
1177C THR* 1.3 73.4 - - - +
1179C ASN* 1.3 65.1 + - - +
1180C MET 4.0 0.3 + - - -
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Residues in contact with ASN1179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066C LYS* 2.8 48.0 + - + +
1067C ILE 3.3 5.9 - - - +
1068C ASN* 3.7 12.4 - - - +
1169C PHE 3.4 0.9 - - - +
1170C TYR* 3.2 7.3 - - - -
1171C SER* 2.9 48.0 + - - +
1172C TRP 3.7 17.2 + - - -
1173C GLY* 4.4 6.8 - - - -
1177C THR 4.2 0.2 - - - -
1178C THR* 1.3 73.6 - - - +
1180C MET* 1.3 59.9 + - - +
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Residues in contact with MET1180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065C GLU 3.8 0.3 - - - -
1066C LYS* 3.3 6.8 + - - -
1067C ILE* 2.9 49.2 + - + +
1069C ILE* 4.0 20.9 - - + -
1168C PHE* 3.6 18.2 - - + -
1169C PHE 3.2 5.6 - - - +
1170C TYR* 3.3 46.4 - - + +
1179C ASN* 1.3 75.5 - - - +
1181C LYS* 1.3 67.4 + - - +
1182C VAL* 4.2 11.7 - - + -
1210C THR* 5.7 0.9 - - - -
1213C LEU* 3.5 25.4 - - + -
1214C VAL* 4.1 17.5 - - - -
1217C LEU* 4.9 1.6 - - + -
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Residues in contact with LYS1181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062C VAL* 3.7 30.2 - - - +
1064C ASP 3.3 12.1 - - - +
1065C GLU* 2.7 40.3 + - + +
1066C LYS 4.8 0.2 - - - +
1167C ARG 3.7 2.1 - - - +
1169C PHE* 2.9 47.4 + - + +
1180C MET* 1.3 79.5 - - - +
1182C VAL* 1.3 63.6 + - - +
1183C VAL* 3.7 15.5 - - + -
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Residues in contact with VAL1182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062C VAL* 3.7 1.4 - - - +
1063C ILE* 2.8 42.1 + - + +
1064C ASP* 3.1 11.3 + - + +
1067C ILE* 5.9 5.4 - - + -
1166C THR* 3.5 27.4 - - + -
1167C ARG 3.3 5.6 - - - +
1168C PHE* 3.4 34.8 - - + -
1180C MET* 4.2 14.6 - - + -
1181C LYS* 1.3 76.6 - - - +
1183C VAL* 1.3 68.7 + - - +
1206C GLN* 5.9 0.2 - - + -
1210C THR* 4.2 19.7 - - + +
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Residues in contact with VAL1183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C ASP* 4.9 10.5 - - + +
1061C THR 3.6 10.8 - - - +
1062C VAL* 3.6 24.2 - - + -
1166C THR* 3.2 4.1 - - - +
1167C ARG* 2.7 64.9 + - + +
1169C PHE* 4.3 10.3 - - + -
1181C LYS* 3.7 20.6 - - + -
1182C VAL* 1.3 79.7 - - - +
1184C THR* 1.3 60.0 + - - +
1185C ASN* 4.7 7.6 + - - +
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Residues in contact with THR1184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C ASP* 3.7 0.2 - - - -
1061C THR* 2.9 39.4 + - - +
1063C ILE* 3.4 32.5 - - + -
1164C VAL* 3.3 21.1 - - - +
1165C HIS 3.1 12.1 + - - -
1166C THR* 3.6 15.3 + - - -
1183C VAL* 1.3 74.1 - - - +
1185C ASN* 1.3 75.5 + - - +
1186C VAL* 5.6 0.3 - - - +
1202C SER* 5.0 1.7 + - - +
1203C ILE* 4.7 11.9 - - + -
1206C GLN* 4.3 10.3 - - + +
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Residues in contact with ASN1185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060C ASP* 3.4 45.4 + - - +
1061C THR* 5.0 2.9 - - - +
1164C VAL* 4.5 0.2 - - - -
1165C HIS* 2.7 62.8 + - - +
1167C ARG* 4.7 12.7 + - - +
1183C VAL* 4.7 6.5 + - - +
1184C THR* 1.3 86.7 + - - +
1186C VAL* 1.3 65.0 + - - +
1187C VAL* 4.1 11.7 - - + +
1203C ILE* 6.5 0.7 - - - -
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Residues in contact with VAL1186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162C PHE* 3.8 28.3 - - + +
1163C SER 3.3 13.5 - - - +
1164C VAL* 3.7 23.8 - - + +
1184C THR* 5.6 0.7 - - - +
1185C ASN* 1.3 78.7 - - - +
1187C VAL* 1.3 71.1 + - - +
1188C TRP* 4.2 12.7 - - + +
1198C ILE 5.1 0.2 - - - +
1199C GLU* 3.8 38.7 + - + +
1202C SER* 4.1 15.3 - - - +
1203C ILE* 5.7 4.0 - - + -
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Residues in contact with VAL1187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162C PHE* 3.0 18.7 + - - -
1163C SER* 3.0 16.4 + - - +
1165C HIS* 3.4 38.6 - - + +
1185C ASN* 4.1 16.2 - - + +
1186C VAL* 1.3 80.8 - - - +
1188C TRP* 1.3 66.1 + - - +
1189C THR* 4.1 4.2 + - - +
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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