Contacts of the strand formed by residues 1061 - 1069 (chain B) 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 THR1061 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1060B ASP* 1.3 78.9 + - - +
1062B VAL* 1.3 64.1 + - - +
1063B ILE* 2.8 14.5 + - - +
1183B VAL* 4.5 2.4 - - - +
1184B THR* 2.8 32.0 + - - +
1185B ASN* 5.5 0.7 - - - -
1199B GLU* 5.7 1.2 + - - -
1203B ILE* 3.9 36.0 - - + +
1207B ARG* 5.5 2.5 - - - +
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Residues in contact with VAL1062 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060B ASP 4.3 0.4 - - - -
1061B THR* 1.3 71.6 - - - +
1063B ILE* 1.3 62.0 + - - +
1064B ASP* 4.1 8.5 - - - +
1065B GLU* 3.7 34.8 - - + +
1181B LYS* 3.7 26.7 - - - +
1182B VAL 4.0 4.3 - - - +
1183B VAL* 4.0 7.2 - - + -
1207B ARG* 4.6 6.6 + - - -
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Residues in contact with ILE1063 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1061B THR* 2.8 7.5 + - - +
1062B VAL* 1.3 74.5 - - - +
1064B ASP* 1.3 76.3 + - - +
1182B VAL* 2.9 37.3 + - + +
1184B THR* 3.6 17.3 - - - +
1203B ILE* 3.2 39.5 - - + +
1206B GLN* 3.4 17.5 - - + -
1207B ARG* 2.8 48.6 + - + +
1210B THR* 4.2 13.0 - - + +
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Residues in contact with ASP1064 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B VAL* 3.5 4.0 - - - -
1063B ILE* 1.3 93.4 - - + +
1065B GLU* 1.3 63.5 + - - +
1067B ILE* 3.2 37.7 - - + +
1180B MET 4.7 1.6 - - - -
1181B LYS* 3.2 2.7 - - - +
1182B VAL* 2.6 39.1 + - + +
1207B ARG* 4.0 10.7 + - - +
1210B THR* 4.6 8.6 + - - +
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Residues in contact with GLU1065 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B VAL* 3.7 18.4 - - + +
1064B ASP* 1.3 79.7 + - - +
1066B LYS* 1.3 78.6 + - + +
1067B ILE* 3.0 3.8 + - - +
1181B LYS* 3.2 48.5 + - + +
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Residues in contact with LYS1066 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065B GLU* 1.3 83.6 - - + +
1067B ILE* 1.3 64.0 + - - +
1068B ASN* 3.9 3.9 + - + +
1179B ASN* 4.3 30.4 - - - +
1180B MET 3.6 9.0 + - - +
1181B LYS* 4.5 1.2 - - - +
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Residues in contact with ILE1067 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1064B ASP* 3.2 43.3 - - + +
1065B GLU 3.0 2.6 + - - -
1066B LYS* 1.3 75.8 - - - +
1068B ASN* 1.3 62.0 + - - +
1069B ILE* 4.0 12.1 - - + -
1179B ASN* 3.4 1.7 - - - -
1180B MET* 2.5 57.4 + - + +
1182B VAL* 6.1 3.1 - - + -
1210B THR* 5.1 6.7 - - - +
1214B VAL* 4.0 39.7 - - + -
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Residues in contact with ASN1068 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1066B LYS* 3.9 5.8 + - + +
1067B ILE* 1.3 75.1 - - - +
1069B ILE* 1.3 69.5 + - - +
1070B PRO* 4.5 3.5 - - - +
1173B GLY* 4.8 1.2 - - - -
1174B ASP 5.2 1.2 + - - +
1177B THR* 3.0 35.4 - - - +
1178B THR 3.0 23.0 + - - +
1179B ASN* 3.1 22.3 + - - +
1218B LYS* 4.5 5.9 - - - +
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Residues in contact with ILE1069 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ILE* 4.0 18.6 - - + +
1068B ASN* 1.3 80.8 - - - +
1070B PRO* 1.3 61.0 - - + +
1071B VAL* 2.5 30.1 + - + -
1076B VAL* 3.4 21.5 - - + -
1177B THR* 3.1 13.7 - - - +
1178B THR* 3.1 25.7 + - + +
1180B MET* 5.0 10.5 - - + -
1214B VAL* 5.0 7.4 - - + -
1217B LEU* 3.4 38.6 - - + -
1218B LYS* 3.9 15.5 - - + -
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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
------------------------------------------------------------
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