Contacts of the strand formed by residues 1271 - 1276 (chain B) in PDB entry 3KQ4
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 LYS1271 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1116B LYS 5.5 7.2 + - - -
1175B THR* 4.3 19.7 - - + -
1176B PHE 3.6 4.3 - - - -
1177B ILE* 3.7 14.4 - - + -
1181B TYR* 3.6 29.2 - - + +
1207B PHE* 3.3 7.4 - - - +
1208B LYS* 3.1 45.7 + - + +
1209B ASP* 3.3 10.1 + - + -
1270B PHE* 1.3 76.3 - - - +
1272B ALA* 1.3 62.0 + - - +
1273B GLU 5.6 0.2 - - - +
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Residues in contact with ALA1272 (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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1175B THR* 3.2 25.8 - - - -
1176B PHE* 3.1 44.8 + - + +
1205B LEU* 4.3 4.7 - - + -
1206B GLU 3.3 11.4 - - - +
1207B PHE* 4.3 15.9 - - + -
1270B PHE* 4.3 4.5 - - + -
1271B LYS* 1.3 76.1 - - - +
1273B GLU* 1.3 64.3 + - - +
1274B TYR 3.6 0.5 + - - -
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Residues in contact with GLU1273 (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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1174B GLY 3.8 8.5 - - - +
1175B THR* 4.1 8.5 - - - +
1205B LEU* 4.0 0.2 - - - -
1206B GLU* 2.9 38.6 + - + +
1207B PHE* 4.8 0.8 - - - +
1208B LYS* 2.9 37.2 + - + +
1271B LYS* 4.1 2.2 + - - +
1272B ALA* 1.3 73.9 - - - +
1274B TYR* 1.3 61.7 + - - +
1275B ARG* 2.7 47.9 + - + +
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Residues in contact with TYR1274 (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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1169B LEU* 3.9 28.9 + - + +
1171B THR* 3.1 44.8 + - - -
1172B SER 4.4 1.1 - - - -
1173B SER* 3.3 6.8 - - - -
1174B GLY* 3.2 55.9 + - - +
1175B THR* 3.6 4.0 - - - -
1176B PHE* 4.1 15.9 - + - -
1195B LEU* 3.7 27.6 - - + -
1203B PHE* 4.3 14.4 - + - -
1204B GLU 3.3 12.8 - - - +
1205B LEU* 4.1 19.1 - - + -
1272B ALA 4.7 0.4 - - - +
1273B GLU* 1.3 76.2 - - - +
1275B ARG* 1.3 63.7 + - - +
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Residues in contact with ARG1275 (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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1172B SER 3.9 1.6 - - - -
1173B SER* 4.0 11.0 - - - -
1203B PHE* 3.6 3.1 - - - +
1204B GLU* 2.8 58.5 + - + +
1206B GLU* 2.8 31.2 + - - -
1273B GLU* 2.7 44.8 + - + +
1274B TYR* 1.3 82.5 - - - +
1276B GLN* 1.3 63.0 + - - +
1277B THR 4.2 0.2 - - - -
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Residues in contact with GLN1276 (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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1172B SER* 3.0 29.3 + - - +
1173B SER* 4.5 0.4 - - - -
1197B SER* 2.8 15.8 + - - -
1198B SER* 3.1 36.3 + - - +
1201B SER* 2.9 29.9 + - - +
1202B ALA 3.5 13.7 - - - +
1203B PHE* 3.2 35.4 - - + -
1253B ASP 4.5 0.2 + - - -
1275B ARG* 1.3 77.3 - - - +
1277B THR* 1.3 58.7 + - - +
1294B ILE* 4.2 15.7 - - + +
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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