Contacts of the strand formed by residues 375 - 382 (chain B) in PDB entry 3GXM
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 375 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B GLN* 3.0 17.4 + - - +
310B VAL* 5.3 1.8 - - + -
324B LEU* 3.9 18.4 - - + -
336B LEU* 3.6 22.7 - - + +
337B PHE* 4.2 0.4 - - - +
338B ALA 3.7 16.4 - - - +
370B ASN* 3.3 40.5 + - + +
371B LEU* 3.4 14.9 - - - +
373B TYR 3.2 14.0 - - - +
374B HIS* 1.3 76.5 - - - +
376B VAL* 1.3 59.7 + - - +
377B GLY 3.2 24.0 - - - +
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Residues in contact with VAL 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLN* 3.9 12.3 - - + -
77B LYS 3.4 24.9 - - - +
78B VAL* 3.4 12.3 - - - +
79B LYS* 2.5 38.4 + - + +
335B MET* 3.9 41.7 - - + -
336B LEU 2.9 20.1 + - - +
337B PHE* 4.1 6.3 - - + -
371B LEU* 5.3 2.2 - - - -
374B HIS 3.6 14.6 - - - +
375B VAL* 1.3 73.2 - - - +
377B GLY* 1.3 57.9 + - - +
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Residues in contact with GLY 377 (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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78B VAL* 5.2 0.9 - - - -
80B GLY 3.3 12.8 - - - -
81B PHE* 5.2 2.9 - - - -
337B PHE* 3.5 22.9 - - - -
338B ALA* 3.2 7.9 + - - +
371B LEU* 5.5 1.3 - - - +
375B VAL* 3.2 23.2 + - - +
376B VAL* 1.3 81.3 - - - +
378B TRP* 1.3 65.1 + - - +
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Residues in contact with TRP 378 (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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80B GLY 3.2 6.3 + - - -
81B PHE* 3.4 42.8 - - + +
82B GLY 3.5 2.9 + - - +
314B LEU* 4.3 2.0 - - + -
337B PHE* 4.1 2.0 - - - -
338B ALA* 3.3 21.7 + - + +
341B ALA* 3.4 28.4 - - + +
363B TYR* 3.7 35.7 - + - -
366B SER* 3.1 30.7 + - - -
367B ILE* 3.5 25.8 - - + +
370B ASN* 3.8 21.7 + - + +
377B GLY* 1.3 72.9 - - - -
379B THR* 1.3 67.0 + - - +
380B ASP* 4.1 13.7 - - - -
420B LEU* 3.7 31.1 - - + +
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Residues in contact with THR 379 (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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82B GLY 3.5 2.9 - - - -
83B GLY* 3.6 29.4 - - - +
118B ILE* 3.9 16.3 - - + +
120B ARG* 4.2 10.3 - - + -
175B LEU* 5.6 0.4 - - + -
337B PHE* 3.1 24.8 - - - -
338B ALA* 2.7 15.7 + - - +
339B SER* 3.4 17.5 - - - +
340B GLU* 3.3 6.1 + - - -
341B ALA* 3.2 21.1 + - - +
378B TRP* 1.3 80.8 - - - +
380B ASP* 1.3 66.9 + - - +
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Residues in contact with ASP 380 (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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82B GLY 2.9 17.4 + - - +
83B GLY* 3.3 13.5 - - - -
84B ALA* 3.4 5.2 + - - +
108B TYR* 4.8 1.9 + - - -
116B TYR* 4.4 3.7 + - - +
339B SER 4.6 2.4 - - - +
340B GLU* 4.8 0.4 - - - -
341B ALA 3.5 3.3 - - - +
363B TYR* 2.4 40.0 + - - -
378B TRP* 4.1 8.4 - - + -
379B THR* 1.3 81.7 - - - +
381B TRP* 1.3 74.3 + - - +
382B ASN 3.7 8.8 - - - +
383B LEU* 4.9 1.9 - - - +
401B PRO* 3.1 28.6 - - - +
420B LEU* 4.2 13.7 - - + +
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Residues in contact with TRP 381 (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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83B GLY* 3.9 0.5 - - - -
84B ALA* 2.9 33.5 + - + -
86B THR* 3.4 25.1 - - + -
120B ARG* 3.9 14.6 - - + -
122B PRO* 4.7 1.8 - - + -
126B CYS* 4.1 5.8 - - - -
127B ASP* 4.1 9.5 + - - -
128B PHE* 3.4 33.5 - + - -
179B TRP* 3.4 33.7 - + - -
340B GLU* 3.8 31.0 + - + -
341B ALA 3.1 17.9 + - - +
342B CYS* 4.0 16.4 - - + -
380B ASP* 1.3 90.4 + - - +
382B ASN* 1.3 81.5 + - - +
383B LEU 3.3 0.2 + - - -
398B VAL* 4.1 15.9 - - + -
399B ASP 5.8 1.6 - - - +
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Residues in contact with ASN 382 (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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84B ALA* 3.9 6.7 - - - -
86B THR* 2.5 35.3 + - - +
88B ALA* 4.1 0.2 - - - +
128B PHE* 3.4 44.8 - - - +
380B ASP* 3.7 8.7 - - - +
381B TRP* 1.3 91.2 - - - +
383B LEU* 1.3 57.7 + - - +
384B ALA 3.7 14.8 - - - +
385B LEU* 3.7 23.8 - - + +
398B VAL* 4.0 2.0 - - - +
399B ASP 5.4 0.8 + - - +
400B SER* 2.9 21.6 + - - -
401B PRO* 3.9 0.3 - - - +
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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