Contacts of the strand formed by residues 1265 - 1270 (chain B) in PDB entry 4DDI
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1045B ASN* 5.8 0.4 + - - -
1085B THR* 2.8 39.2 + - - -
1087B PRO* 3.6 25.7 - - + +
1091B SER* 2.8 28.8 + - - -
1260B LEU 3.7 0.3 - - - +
1261B TYR* 3.6 3.5 - - - -
1262B ARG* 2.8 52.8 + - + +
1263B PRO 3.2 3.3 - - - +
1264B GLY* 1.3 82.0 + - - +
1266B TYR* 1.3 70.5 + - - +
1267B ASP* 3.2 31.1 + - - +
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Residues in contact with TYR1266 (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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1085B THR* 3.2 21.8 + - - +
1091B SER* 3.7 5.0 - - - +
1092B PHE* 3.8 48.2 - + + +
1095B ALA* 4.7 4.0 - - + -
1215B SER* 4.2 23.8 + - - -
1216B ASP* 4.7 3.1 + - - -
1220B ILE* 3.2 34.5 - - + +
1233B VAL* 4.5 12.7 - - + +
1259B LEU* 4.3 12.6 - - + -
1260B LEU 3.4 7.9 - - - -
1261B TYR* 3.7 35.6 - + - -
1264B GLY 5.3 1.6 - - - -
1265B HIS* 1.3 88.9 + - - +
1267B ASP* 1.3 71.1 + - - +
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Residues in contact with ASP1267 (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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1082B ILE* 4.4 8.5 - - + -
1083B ARG 3.6 9.9 - - - +
1084B LYS* 3.3 11.0 - - - +
1085B THR* 3.2 27.1 + - - -
1095B ALA* 4.4 1.8 - - - -
1259B LEU* 3.3 11.4 - - - +
1260B LEU* 2.9 39.9 + - + +
1262B ARG* 2.7 37.0 + - - -
1265B HIS* 3.2 15.1 + - - -
1266B TYR* 1.3 79.1 + - - +
1268B ILE* 1.3 65.5 + - - +
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Residues in contact with ILE1268 (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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1048B VAL* 5.6 1.8 - - + -
1082B ILE* 3.2 6.4 - - - +
1083B ARG* 2.9 66.4 + - + +
1085B THR* 5.2 3.6 - - + -
1095B ALA* 3.7 35.2 - - + +
1098B PHE* 4.0 14.4 - - + -
1099B SER* 3.8 20.4 - - - +
1258B TYR 3.6 10.8 - - - +
1259B LEU* 4.1 6.3 - - + -
1267B ASP* 1.3 79.9 - - - +
1269B LEU* 1.3 65.2 + - - +
1270B TYR* 3.2 25.7 - - + +
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Residues in contact with LEU1269 (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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1054B LEU* 5.1 1.3 - - + -
1075B LEU* 4.0 21.8 - - + -
1079B TYR* 3.7 43.5 - - + -
1081B TYR 3.5 6.7 - - - +
1082B ILE* 3.7 22.7 - - + -
1234B GLU* 3.8 9.6 - - + -
1258B TYR* 3.0 30.7 + - + +
1259B LEU 3.6 13.5 - - - +
1260B LEU* 3.6 36.8 - - + +
1268B ILE* 1.3 72.7 - - - +
1270B TYR* 1.3 75.9 + - - +
1271B LYS 4.3 0.2 - - - -
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Residues in contact with TYR1270 (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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1051B ARG* 3.5 34.8 - - + +
1079B TYR* 3.5 4.5 - - - -
1080B SER* 2.8 30.8 + - - -
1081B TYR* 2.9 38.7 + - + -
1082B ILE 4.4 1.1 - - - -
1083B ARG* 2.8 43.1 + - + -
1099B SER* 4.9 6.7 - - - -
1102B GLU* 2.4 37.4 + - - -
1258B TYR* 5.4 0.9 - + - -
1268B ILE* 3.2 20.7 - - + +
1269B LEU* 1.3 84.1 - - - +
1271B LYS* 1.3 57.8 + - - +
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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