Contacts of the strand formed by residues 1178 - 1188 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068A ASN* 4.3 0.4 - - - -
1069A ILE* 2.3 51.0 + - + +
1071A VAL 2.8 21.1 + - - -
1072A PRO 3.2 0.3 + - - -
1073A LEU* 3.0 45.7 + - + +
1076A VAL* 4.3 9.4 - - + -
1170A TYR* 4.1 19.7 - - + -
1171A SER 3.7 6.3 - - - +
1177A THR* 1.3 78.7 + - - +
1179A ASN* 1.3 67.1 + - - +
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Residues in contact with ASN1179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066A LYS* 3.0 38.8 + - + +
1067A ILE 2.9 17.5 - - - +
1068A ASN* 4.3 2.4 - - - +
1169A PHE 3.8 0.7 - - - +
1170A TYR* 3.6 1.0 - - - -
1171A SER* 2.8 66.0 + - - -
1172A TRP 4.4 5.3 + - - -
1173A GLY* 3.9 14.8 - - - -
1174A ASP* 4.9 0.7 + - - +
1177A THR* 4.2 7.1 - - - +
1178A THR* 1.3 75.4 - - - +
1180A MET* 1.3 59.0 + - - +
1181A LYS 4.5 0.2 + - - -
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Residues in contact with MET1180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064A ASP* 4.1 2.1 - - - +
1066A LYS* 3.8 4.8 - - - -
1067A ILE* 3.0 47.0 + - + +
1069A ILE* 4.4 15.0 - - + -
1168A PHE* 4.5 2.7 - - + -
1169A PHE 3.0 11.7 - - - +
1170A TYR* 3.6 37.2 - - + +
1178A THR 4.2 0.2 - - - -
1179A ASN* 1.3 75.4 - - - +
1181A LYS* 1.3 61.0 + - - +
1182A VAL* 3.7 25.8 - - + -
1210A THR* 4.1 3.4 - - + -
1213A LEU* 3.6 28.9 - - + -
1214A VAL* 3.8 21.5 - - + -
1217A LEU* 4.7 3.4 - - - -
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Residues in contact with LYS1181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A VAL* 3.7 26.2 - - + +
1064A ASP 3.1 18.8 - - - +
1065A GLU* 3.2 44.6 + - + +
1167A ARG 3.8 0.3 - - - +
1168A PHE* 3.7 0.7 - - - -
1169A PHE* 2.9 44.9 + - + +
1180A MET* 1.3 73.9 - - - +
1182A VAL* 1.3 66.6 + - - +
1183A VAL* 4.0 19.7 - - + -
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Residues in contact with VAL1182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062A VAL* 3.8 0.5 - - - -
1063A ILE* 2.8 40.5 + - + +
1064A ASP* 3.0 13.7 + - + +
1166A THR* 3.5 26.7 - - + -
1167A ARG 3.4 4.0 - - - +
1168A PHE* 4.0 11.4 - - + -
1180A MET* 3.7 19.5 - - + -
1181A LYS* 1.3 80.9 - - - +
1183A VAL* 1.3 64.9 + - - +
1206A GLN* 3.9 5.2 - - - +
1210A THR* 3.7 38.4 - - + +
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Residues in contact with VAL1183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A THR* 3.5 32.8 - - + +
1062A VAL* 4.2 9.0 - - + -
1165A HIS 3.8 0.5 - - - +
1166A THR* 3.3 0.9 - - - -
1167A ARG* 2.7 45.3 + - + +
1169A PHE* 4.5 20.4 - - + -
1181A LYS* 4.0 29.4 - - + -
1182A VAL* 1.3 79.2 - - - +
1184A THR* 1.3 64.9 + - - +
1185A ASN* 5.1 2.7 - - - +
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Residues in contact with THR1184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A THR* 2.8 32.2 + - - +
1063A ILE* 3.3 27.0 - - + +
1164A VAL* 4.5 9.7 - - - +
1165A HIS 3.0 13.7 - - - -
1166A THR* 3.2 23.1 - - + +
1183A VAL* 1.3 79.1 - - - +
1185A ASN* 1.3 68.1 + - - +
1202A SER* 4.8 0.9 - - - -
1203A ILE* 3.6 23.2 + - - +
1206A GLN* 3.4 14.9 - - + +
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Residues in contact with ASN1185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061A THR* 4.8 9.4 - - + +
1164A VAL* 4.9 0.7 - - - -
1165A HIS* 3.0 34.3 + - - +
1167A ARG* 3.4 24.1 + - - +
1183A VAL* 5.1 2.9 - - - +
1184A THR* 1.3 81.9 + - - +
1186A VAL* 1.3 67.1 + - - +
1187A VAL* 3.5 24.7 - - - +
1199A GLU* 5.2 1.3 - - - -
1203A ILE* 5.1 4.5 - - - -
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Residues in contact with VAL1186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162A PHE* 3.6 30.1 - - + -
1163A SER 3.5 12.3 - - - +
1164A VAL* 4.4 4.5 - - + +
1185A ASN* 1.3 77.8 + - - +
1187A VAL* 1.3 62.1 + - - +
1188A TRP* 3.7 27.1 - - + -
1198A ILE* 4.6 0.9 - - + -
1199A GLU* 3.8 42.7 + - - +
1202A SER* 3.3 31.0 - - - +
1203A ILE* 5.2 1.6 - - + -
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Residues in contact with VAL1187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1162A PHE* 3.1 5.9 - - - +
1163A SER* 3.0 33.1 + - - +
1165A HIS* 3.7 36.1 - - + +
1185A ASN* 3.5 22.4 + - - +
1186A VAL* 1.3 71.5 - - - +
1188A TRP* 1.3 69.9 + - - +
1189A THR* 5.1 8.2 - - + +
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Residues in contact with TRP1188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1158A TYR 5.0 0.4 - - - -
1161A SER* 3.3 22.4 - - - -
1162A PHE* 3.4 23.1 - + + -
1186A VAL* 3.7 24.0 - - + +
1187A VAL* 1.3 79.0 - - - +
1189A THR* 1.3 65.4 + - - +
1190A GLY 3.6 19.5 - - - +
1192A SER* 4.2 15.5 - - - -
1195A LYS* 3.4 55.8 - - + +
1198A ILE* 3.5 30.5 - - + -
1199A GLU* 3.0 27.1 + - + -
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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