Contacts of the strand formed by residues 437 - 442 (chain A) in PDB entry 2GLQ
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 VAL 437 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET 4.9 0.2 - - - +
45A GLY* 4.3 7.0 - - - -
46A VAL* 4.8 4.3 - - - -
79A LEU* 3.4 7.7 - - - -
80A SER* 2.8 41.8 + - - +
82A THR* 3.8 14.6 - - + -
355A THR* 4.1 1.1 - - - +
356A ALA* 3.4 34.1 - - + +
358A HIS* 3.7 33.4 - - - +
359A SER* 3.9 8.5 - - - +
435A GLU 3.8 7.9 - - - +
436A ASP* 1.3 80.3 - - - +
438A ALA* 1.3 65.9 + - - +
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Residues in contact with ALA 438 (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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44A MET* 5.5 2.7 + - - +
46A VAL* 4.5 16.8 - - + +
49A VAL* 6.0 2.9 - - + -
77A VAL* 5.0 7.0 - - + -
78A ALA 3.5 6.5 - - - +
79A LEU* 4.6 4.9 - - + -
354A VAL 4.0 0.4 - - - +
355A THR* 2.8 30.3 + - - -
356A ALA* 3.9 2.9 + - - +
437A VAL* 1.3 76.1 - - - +
439A VAL* 1.3 57.9 + - - +
440A PHE* 3.8 30.6 - - + -
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Residues in contact with VAL 439 (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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76A TYR 3.6 0.7 - - - +
77A VAL* 3.2 9.2 - - - +
78A ALA* 2.9 39.0 + - + +
80A SER* 3.7 21.5 - - - +
353A LEU* 4.1 12.6 - - + -
354A VAL 3.4 8.7 - - - +
355A THR* 3.6 13.7 - - - +
438A ALA* 1.3 76.3 - - - +
440A PHE* 1.3 66.7 + - - +
449A VAL* 3.9 22.3 - - + +
458A ILE* 3.4 33.4 - - + -
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Residues in contact with PHE 440 (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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44A MET* 4.7 7.2 - - + -
49A VAL* 4.6 15.0 - - + -
53A ARG* 6.1 0.2 - - - -
71A MET* 3.4 47.6 - - + +
72A ASP* 4.5 9.9 - - - -
74A PHE* 3.7 22.2 - - + -
76A TYR 3.3 5.2 - - - -
77A VAL* 3.6 24.0 - - + -
353A LEU* 3.2 5.7 - - - +
354A VAL* 2.8 55.8 + - + +
438A ALA* 3.8 25.8 - - + -
439A VAL* 1.3 75.2 - - - +
441A ALA* 1.3 61.9 + - - +
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Residues in contact with ALA 441 (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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74A PHE* 3.6 3.9 - - - +
75A PRO* 3.4 9.0 - - - +
76A TYR* 2.7 36.5 + - - +
352A SER 3.3 4.0 - - - -
353A LEU* 3.4 24.0 - - + -
440A PHE* 1.3 76.7 - - - +
442A ARG* 1.3 62.0 + - - +
446A ALA* 3.8 13.7 - - + +
449A VAL* 3.8 26.9 - - + -
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Residues in contact with ARG 442 (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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70A ALA 4.7 0.6 + - - -
73A ARG* 3.4 36.4 + - - +
74A PHE* 3.7 34.2 - - + -
75A PRO* 3.7 23.3 - - + +
342A GLY* 6.2 3.8 - - - -
347A GLU* 2.9 43.9 + - + +
350A THR 3.6 0.8 - - - +
351A LEU* 3.5 3.5 - - - +
352A SER* 2.9 43.7 + - - +
441A ALA* 1.3 75.6 - - - +
443A GLY* 1.3 59.2 + - - +
446A ALA* 3.5 7.2 - - - -
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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