Contacts of the strand formed by residues 455 - 459 (chain A) in PDB entry 1Q2L
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 455 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A SER* 4.1 4.8 + - - +
188A THR* 2.9 49.4 + - - +
189A ILE* 3.2 23.0 - - - +
270A VAL* 4.3 3.1 - - - -
274A GLN* 3.0 32.6 + - - +
275A LYS* 4.5 4.7 - - - -
277A ILE* 3.6 19.2 - - + +
279A ILE* 3.8 15.5 - - + +
291A ARG 3.5 2.3 - - - +
293A GLU* 2.7 67.9 + - - +
295A ARG* 3.6 25.7 - - - +
453A ASN 5.0 2.0 - - - +
454A ALA* 1.3 75.8 - - - +
456A ILE* 1.3 61.4 + - - +
457A TRP* 3.7 4.0 + - - -
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Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ILE 2.9 12.2 + - - +
278A ILE* 3.2 9.4 - - + +
279A ILE* 2.7 29.9 + - - +
290A LEU* 3.5 30.7 - - + -
291A ARG 3.3 5.8 - - - +
292A VAL* 4.4 13.5 - - + -
369A VAL* 4.3 5.8 - - + -
373A PHE* 4.2 19.7 - - + -
451A PRO 5.0 0.4 - - - +
454A ALA* 3.9 17.7 - - + -
455A ARG* 1.3 74.2 - - - +
457A TRP* 1.3 58.3 + - - +
458A TYR* 3.6 13.3 + - + -
481A ILE* 4.1 7.4 - - + -
489A TRP* 3.6 35.2 - - + -
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Residues in contact with TRP 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 3.7 26.0 - - + -
184A VAL* 3.1 36.6 - - + -
185A SER* 3.5 18.8 - - - -
279A ILE* 3.3 36.7 - - + +
281A TYR* 3.8 29.2 - + + -
289A VAL 3.6 0.7 - - - +
290A LEU* 3.4 12.8 - - - +
291A ARG* 2.7 59.9 + - + +
293A GLU* 2.8 28.9 + - + -
455A ARG* 3.7 11.4 + - - -
456A ILE* 1.3 71.4 - - - +
458A TYR* 1.3 60.7 + - - +
459A ILE* 3.7 17.5 - - + -
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Residues in contact with TYR 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ILE* 3.8 31.2 - - + +
279A ILE 2.9 10.1 + - - +
280A HIS* 3.9 16.6 - - + -
281A TYR 3.1 22.0 + - - -
289A VAL 4.2 1.3 - - - -
290A LEU* 3.4 30.1 - - + -
365A ARG* 3.4 46.2 - - + +
366A ASP* 4.1 10.6 + - - -
369A VAL* 4.1 8.2 - - + +
456A ILE* 3.6 14.8 + - + -
457A TRP* 1.3 73.0 - - - +
459A ILE* 1.3 60.4 + - - +
463A GLU* 3.3 21.9 - - - +
489A TRP* 3.6 22.9 - + - -
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Residues in contact with ILE 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 4.2 13.9 - - - -
281A TYR* 3.4 31.0 - - + +
283A PRO* 3.8 19.3 - - + -
287A ARG* 3.9 19.7 - - + +
288A LYS* 3.3 2.4 - - - -
289A VAL* 2.9 56.1 + - + +
291A ARG* 3.6 27.6 - - - +
362A LEU* 4.8 2.6 - - - +
365A ARG* 4.7 0.9 + - - +
457A TRP* 4.0 18.6 - - + -
458A TYR* 1.3 75.5 - - - +
460A SER* 1.3 66.6 + - - +
463A GLU* 4.0 0.2 - - - -
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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