Contacts of the strand formed by residues 260 - 265 (chain A) in PDB entry 1QFM
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 ARG 260 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A TRP* 3.3 45.4 - - - -
249A LEU 4.1 0.2 - - - -
250A SER* 3.3 1.4 - - - -
251A ILE* 2.9 38.2 + - + -
259A ASN* 1.3 87.1 + - - +
261A LEU* 1.3 60.1 + - - +
262A TRP* 4.1 11.5 - - - +
283A ILE 3.3 10.1 - - - +
284A ASP* 2.7 53.6 + - - -
285A ASN* 3.2 26.4 - - - +
286A PHE* 3.7 28.0 - - + -
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Residues in contact with LEU 261 (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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239A GLU* 5.7 1.1 - - - +
248A LEU* 4.6 20.4 - - + -
249A LEU 3.4 7.2 - - - +
250A SER* 3.7 22.9 - - - +
259A ASN* 4.0 11.2 - - - +
260A ARG* 1.3 73.2 - - - +
262A TRP* 1.3 75.3 + - - +
263A TYR* 4.8 2.0 - - + -
282A LEU* 3.4 27.3 + - + +
283A ILE* 2.9 52.9 + - + +
290A TYR* 4.1 14.6 - - + +
292A TYR* 5.9 1.1 - - + +
302A PHE* 4.0 27.6 - - + -
318A PHE* 5.3 0.4 - - + -
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Residues in contact with TRP 262 (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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228A PHE* 3.9 15.5 - + - -
234A TRP* 4.5 11.7 - + - -
248A LEU* 3.6 1.9 - - - -
249A LEU* 2.8 49.6 + - + +
251A ILE* 3.5 23.2 - - + +
260A ARG* 4.1 5.3 - - + +
261A LEU* 1.3 89.6 - - - +
263A TYR* 1.3 62.9 + - - +
279A TRP* 3.9 27.1 - + + -
280A VAL 3.2 9.2 - - - +
281A LYS* 3.6 44.2 - - + +
283A ILE 3.9 8.0 + - - -
284A ASP* 2.9 26.5 + - - -
791A GOL 3.7 40.4 - - - -
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Residues in contact with TYR 263 (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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246A TYR* 3.8 17.7 - + + -
247A VAL 3.2 10.1 - - - +
248A LEU* 3.8 17.7 - - + -
261A LEU* 4.8 1.1 - - + -
262A TRP* 1.3 76.0 - - - +
264A CYS* 1.3 60.4 + - - +
265A ASP* 4.2 8.7 - - + -
279A TRP* 3.5 5.2 - - - -
280A VAL* 2.8 76.1 + - + +
282A LEU* 4.0 21.7 - - + +
318A PHE* 3.5 63.1 + + + +
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Residues in contact with CYS 264 (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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246A TYR* 3.2 6.7 - - - -
247A VAL* 2.9 34.5 + - + +
263A TYR* 1.3 74.5 - - - +
265A ASP* 1.3 70.9 + - - +
266A LEU* 3.2 11.5 + - - +
269A GLU* 3.1 35.0 - - - -
277A LEU* 3.8 24.0 - - + -
278A LYS* 4.3 9.4 - - - +
279A TRP* 3.8 20.8 - - + -
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Residues in contact with ASP 265 (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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245A ARG* 2.9 46.0 + - - +
246A TYR* 3.8 24.6 + - + -
263A TYR* 4.2 9.0 - - + -
264A CYS* 1.3 75.6 - - - +
266A LEU* 1.3 56.5 + - - +
267A GLN* 3.2 13.9 + - - +
268A GLN* 2.9 44.3 + - + +
269A GLU* 3.7 3.1 + - - +
278A LYS 5.1 1.8 + - - -
280A VAL* 5.7 1.9 - - + +
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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