Contacts of the strand formed by residues 281 - 286 (chain B) in PDB entry 1K7E
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 GLY 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A LEU* 5.2 2.4 - - - +
14B GLY 3.3 12.3 - - - +
16B TYR* 2.9 49.2 + - - +
17B VAL* 4.3 3.8 - - - -
174B LEU* 5.6 0.4 - - - +
194B PRO* 3.4 19.0 - - - +
279B TYR* 3.0 1.2 - - - +
280B PHE* 1.3 75.6 - - - +
282B MET* 1.3 64.8 + - - +
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Residues in contact with MET 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY* 3.4 16.2 - - - +
16B TYR* 3.9 8.6 - - - +
192B ALA* 4.0 8.3 - - + -
193B GLY 3.3 31.6 - - - +
278B ILE* 3.3 1.4 - - - -
279B TYR 2.8 43.6 + - - +
280B PHE* 4.1 4.7 - - + +
281B GLY* 1.3 87.2 - - - +
283B LYS* 1.3 58.5 + - - +
284B ALA* 3.6 8.5 - - + -
286B MET* 3.6 4.3 - - + +
306B PHE* 4.1 7.4 - - + -
308B SER* 3.0 33.2 - - - +
309B VAL 3.1 20.4 - - - +
311B PRO* 3.9 21.3 - - - -
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Residues in contact with LYS 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.8 27.4 - - + -
111A ILE* 6.0 1.6 - - - +
138A PRO* 5.9 4.8 - - - +
139A PHE* 6.3 0.6 - - - -
8B TYR* 4.9 3.3 + - + -
11B GLU* 3.5 42.9 + - + +
12B PHE* 3.3 7.3 - - + +
13B GLY* 2.8 37.5 + - - +
16B TYR* 3.6 26.9 + - + -
276B VAL* 3.5 18.2 - - + -
277B GLY 3.1 8.7 - - - +
278B ILE* 4.1 11.6 - - + +
282B MET* 1.3 70.1 - - - +
284B ALA* 1.3 66.8 - - - +
311B PRO* 4.6 0.2 - - - +
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Residues in contact with ALA 284 (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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12B PHE* 4.2 5.8 - - - -
276B VAL* 4.1 3.4 - - - -
277B GLY 2.9 28.0 + - - +
282B MET* 3.6 22.9 + - + -
283B LYS* 1.3 75.7 - - - +
285B PRO* 1.3 74.7 - - + +
286B MET* 3.3 5.7 - - + +
308B SER* 3.7 3.8 - - - +
309B VAL* 3.5 24.7 - - + +
311B PRO* 4.9 7.2 - - + -
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Residues in contact with PRO 285 (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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12B PHE* 4.0 11.7 - - + -
270B PRO* 3.0 30.5 - - - +
271B LEU* 3.7 21.1 - - + +
274B GLY 5.2 0.2 - - - -
275B ARG 3.7 14.1 - - - +
276B VAL* 4.3 6.7 - - + -
284B ALA* 1.3 85.4 - - + +
286B MET* 1.3 58.6 + - - +
308B SER* 2.8 27.4 + - - -
309B VAL* 3.9 11.8 + - + -
314B ALA* 3.9 24.5 - - + -
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Residues in contact with MET 286 (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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104A ASN* 4.9 0.2 - - - +
270B PRO* 3.9 5.4 - - - +
274B GLY* 3.7 5.2 - - - -
275B ARG 3.1 22.5 + - - +
277B GLY* 3.5 27.1 - - - +
279B TYR* 3.6 45.1 - - + +
282B MET* 3.6 9.9 - - + +
284B ALA* 3.3 25.4 - - + +
285B PRO* 1.3 72.6 - - - +
287B MET* 1.3 63.6 + - - +
288B GLN* 3.4 22.9 + - + +
294B ILE* 4.1 15.9 - - + -
307B PRO 3.5 5.4 - - - +
308B SER* 3.4 26.0 - - - +
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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