Contacts of the strand formed by residues 508 - 515 (chain B) in PDB entry 3GQL
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 508 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496B GLU* 3.5 45.5 - - + +
497B ALA 3.5 4.9 - - - +
498B ILE* 4.5 19.7 - - + -
506B ASN 5.5 1.8 - - - +
507B ARG* 1.3 80.3 - - - +
509B THR* 1.3 68.4 + - - +
510B LYS* 5.8 0.4 - - + -
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Residues in contact with THR 509 (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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496B GLU* 3.4 3.1 - - - -
497B ALA* 2.8 33.8 + - - +
500B LEU* 3.5 39.3 - - + +
507B ARG* 4.7 4.5 + - - +
508B VAL* 1.3 82.5 + - - +
510B LYS* 1.3 76.3 + - - +
511B VAL* 3.6 1.1 + - + -
548B LEU* 5.5 2.2 - - + -
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Residues in contact with LYS 510 (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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494B LEU* 3.8 36.1 - - + +
495B ALA 3.7 3.1 - - - +
496B GLU* 3.6 32.5 - - + +
508B VAL* 5.8 0.7 - - + -
509B THR* 1.3 80.5 - - - +
511B VAL* 1.3 65.8 + - - +
548B LEU* 5.2 0.7 - - - +
562B GLU* 5.4 0.2 - - - -
563B TYR* 3.6 33.0 + - + +
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Residues in contact with VAL 511 (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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478B LEU* 4.3 9.4 - - + -
494B LEU* 3.4 6.6 - - - +
495B ALA* 3.0 48.1 + - + +
497B ALA* 4.1 15.3 - - + +
500B LEU* 3.8 19.7 - - + -
509B THR* 4.1 4.3 - - + +
510B LYS* 1.3 81.8 - - - +
512B ALA* 1.3 61.1 + - - +
513B VAL* 4.3 2.5 - - + -
548B LEU* 3.6 26.5 - - + -
560B ILE* 3.8 21.3 - - + -
561B VAL 3.6 7.9 - - - +
563B TYR* 3.8 9.4 - - - +
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Residues in contact with ALA 512 (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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1B GQL 3.8 26.5 - - + +
484B LEU* 3.9 11.0 - - + -
492B VAL* 3.8 17.9 - - + -
493B VAL 3.7 5.2 - - - -
511B VAL* 1.3 72.5 - - - +
513B VAL* 1.3 60.9 + - - +
559B VAL 3.5 1.4 - - - +
560B ILE* 3.7 1.0 - - - -
561B VAL* 2.9 47.4 + - + +
562B GLU 3.9 2.2 - - - +
563B TYR* 4.1 1.5 - - - +
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Residues in contact with VAL 513 (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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478B LEU* 3.9 23.3 - - + -
480B LEU* 4.1 10.1 - - + -
491B GLN 3.6 2.6 - - - +
492B VAL* 3.4 2.4 - - - -
493B VAL* 2.9 37.1 + - + +
495B ALA* 3.6 29.8 - - + -
511B VAL* 4.3 5.6 - - + -
512B ALA* 1.3 75.0 - - - +
514B LYS* 1.3 61.6 + - - +
515B MET* 4.5 1.5 - - - +
558B TYR* 3.6 45.1 - - + -
559B VAL 3.7 4.0 - - - +
560B ILE* 4.4 6.5 - - + -
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Residues in contact with LYS 514 (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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1B GQL 3.4 32.5 - - + -
487B GLY* 5.4 6.8 - - - -
488B ALA 5.8 0.2 - - - +
489B PHE* 3.5 24.9 - - - -
490B GLY* 4.1 17.9 - - - +
491B GLN 3.9 7.2 - - - +
492B VAL* 4.0 17.5 - - + +
512B ALA 3.8 1.6 + - - +
513B VAL* 1.3 71.8 - - - +
515B MET* 1.3 68.0 + - - +
528B LEU* 4.1 13.5 - - + +
531B GLU* 3.0 34.3 + - - +
557B LEU 3.8 0.7 - - - +
558B TYR* 3.7 2.9 - - - -
559B VAL* 3.0 47.7 + - + +
641B ASP* 4.5 6.3 + - - -
644B LEU* 5.4 0.2 - - - +
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Residues in contact with MET 515 (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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480B LEU* 4.9 6.3 - - + -
490B GLY* 3.3 4.7 - - - -
491B GLN* 2.7 67.2 + - - +
493B VAL* 4.4 22.2 - - - -
513B VAL* 4.8 2.2 - - - +
514B LYS* 1.3 76.8 - - - +
516B LEU* 1.3 68.5 + - - +
528B LEU* 4.2 6.7 - - - -
556B PRO* 5.5 7.2 - - + -
557B LEU 3.8 7.9 - - - +
558B TYR* 3.6 43.1 - - + +
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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