Contacts of the strand formed by residues 1265 - 1270 (chain A) in PDB entry 4DDG
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 HIS1265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1084A LYS* 5.5 0.8 - - - +
1085A THR* 3.0 30.6 + - - -
1086A ARG 3.6 15.9 - - - -
1087A PRO* 3.7 24.7 - - + +
1091A SER* 3.6 9.7 + - - -
1260A LEU 3.8 0.5 - - - +
1261A TYR* 3.8 4.0 - - - -
1262A ARG* 2.7 53.6 + - + +
1263A PRO 3.2 4.2 - - - +
1264A GLY* 1.3 81.3 + - - +
1266A TYR* 1.3 77.2 + - - +
1267A ASP* 3.2 31.4 + - - +
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Residues in contact with TYR1266 (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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1085A THR* 3.1 21.8 + - - -
1091A SER* 3.5 15.5 + - - +
1092A PHE* 3.6 42.4 - + + +
1095A ALA* 5.0 4.7 - - + -
1215A SER* 4.0 20.0 + - - -
1216A ASP* 4.7 5.2 - - - -
1217A HIS 5.0 0.3 + - - -
1220A ILE* 3.3 34.3 - - + +
1233A VAL* 4.6 8.1 - - + -
1259A LEU* 4.7 13.5 - - + -
1260A LEU 3.5 3.6 - - - -
1261A TYR* 3.6 40.1 - + + -
1264A GLY 5.8 0.9 - - - -
1265A HIS* 1.3 84.3 + - - +
1267A ASP* 1.3 68.7 + - - +
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Residues in contact with ASP1267 (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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1082A ILE* 4.4 10.8 - - + -
1083A ARG 3.9 7.4 - - - +
1084A LYS* 3.4 27.9 - - - +
1085A THR* 3.5 3.6 + - - -
1095A ALA* 4.6 1.8 - - - -
1259A LEU* 3.3 13.6 - - - +
1260A LEU* 2.8 41.2 + - + +
1262A ARG* 2.9 32.5 + - - -
1265A HIS* 3.2 26.8 + - - +
1266A TYR* 1.3 75.8 - - - +
1268A ILE* 1.3 64.6 + - - +
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Residues in contact with ILE1268 (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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1048A VAL* 5.3 0.7 - - + -
1082A ILE* 3.3 9.0 - - - +
1083A ARG* 2.9 53.4 + - + +
1085A THR* 4.7 6.3 - - + -
1095A ALA* 3.7 39.5 - - + +
1098A PHE* 3.6 31.4 - - + -
1099A SER* 3.7 19.7 - - - -
1258A TYR 3.8 9.4 - - - +
1259A LEU* 4.2 1.3 - - + -
1267A ASP* 1.3 72.6 - - - +
1269A LEU* 1.3 66.1 + - - +
1270A TYR* 3.6 21.1 - - + -
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Residues in contact with LEU1269 (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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1054A LEU* 4.6 7.6 - - + -
1075A LEU* 4.0 19.3 - - + -
1079A TYR* 3.6 42.8 - - + -
1081A TYR 3.7 9.0 - - - +
1082A ILE* 3.7 22.7 - - + -
1234A GLU* 4.2 6.3 - - + -
1258A TYR* 3.0 39.0 + - + +
1259A LEU 4.5 0.9 - - - -
1260A LEU* 3.5 35.9 - - + +
1267A ASP 4.1 0.2 + - - -
1268A ILE* 1.3 84.8 - - - +
1270A TYR* 1.3 66.4 + - - +
1271A LYS 4.2 0.4 - - - -
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Residues in contact with TYR1270 (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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1051A ARG* 4.0 25.6 - - + +
1079A TYR* 3.8 3.6 - - - +
1080A SER* 3.1 6.2 + - - -
1081A TYR* 2.9 62.5 + - + +
1082A ILE 4.6 0.4 - - - -
1083A ARG* 2.5 49.2 + - + -
1098A PHE* 3.6 1.4 - - - -
1099A SER* 6.2 0.2 - - - -
1102A GLU* 2.3 42.3 + - - -
1258A TYR* 5.3 0.7 - - - -
1268A ILE* 3.6 23.5 - - + +
1269A LEU* 1.3 78.8 - - - +
1271A LYS* 1.3 63.9 + - - +
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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