Contacts of the strand formed by residues 491 - 498 (chain C) 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 GLN 491 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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483C PRO* 5.7 0.2 - - - -
485C GLY 3.8 4.5 - - - -
486C GLU* 3.2 41.4 + - + +
487C GLY 4.7 0.2 - - - +
490C GLY* 1.3 75.6 - - - +
492C VAL* 1.3 64.9 + - - +
493C VAL* 4.4 14.3 - - + +
514C LYS* 4.4 3.0 - - - +
515C MET* 2.8 71.9 + - + +
516C LEU 4.5 4.3 - - - +
517C LYS* 3.2 27.2 - - + +
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Residues in contact with VAL 492 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C GQL 3.0 65.3 - - + -
483C PRO* 3.7 2.3 - - - +
484C LEU* 2.9 20.6 + - + -
485C GLY 2.9 14.6 + - - +
491C GLN* 1.3 77.0 - - - +
493C VAL* 1.3 71.5 + - - +
512C ALA* 4.0 21.8 - - + -
513C VAL 3.2 14.8 - - - +
514C LYS* 4.0 17.0 - - + +
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Residues in contact with VAL 493 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C LEU* 4.2 23.1 - - + -
481C GLY 4.3 7.9 - - - +
482C LYS 3.9 1.3 - - - +
483C PRO* 3.8 20.0 - - + -
484C LEU* 3.7 11.2 - - - +
491C GLN* 4.4 15.9 - - + +
492C VAL* 1.3 81.3 - - - +
494C LEU* 1.3 65.4 + - - +
512C ALA* 3.5 3.6 - - - -
513C VAL* 2.8 49.3 + - + +
515C MET* 4.4 17.7 - - + -
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Residues in contact with LEU 494 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C GLY* 2.8 30.1 + - - -
482C LYS* 2.7 29.1 + - + +
484C LEU* 3.7 16.2 - - + +
493C VAL* 1.3 71.9 - - - +
495C ALA* 1.3 61.0 + - - +
496C GLU* 6.1 0.4 - - + -
510C LYS* 3.9 22.4 - - + +
511C VAL 3.4 13.0 - - - +
563C TYR* 3.3 58.8 - - + +
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Residues in contact with ALA 495 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C LEU* 4.1 7.9 - - + -
479C VAL 3.0 21.1 - - - +
480C LEU* 3.9 10.1 - - + -
481C GLY* 4.2 0.4 - - - +
493C VAL* 3.7 0.6 + - + -
494C LEU* 1.3 78.2 - - - +
496C GLU* 1.3 64.2 + - - +
510C LYS* 3.6 3.6 - - - -
511C VAL* 2.7 37.9 + - - +
513C VAL* 3.4 28.9 - - + -
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Residues in contact with GLU 496 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C LEU* 4.3 2.0 - - - -
479C VAL* 2.9 48.5 + - + +
494C LEU* 6.1 0.7 - - + -
495C ALA* 1.3 78.8 - - - +
497C ALA* 1.3 62.1 + - - +
498C ILE* 3.6 3.1 + - - +
508C VAL* 3.4 29.3 - - + +
509C THR 3.1 3.6 - - - +
510C LYS* 3.2 36.4 - - + +
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Residues in contact with ALA 497 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C LEU* 4.3 9.9 - - + -
477C ARG 3.5 9.0 - - - +
478C LEU* 4.1 15.3 - - + -
496C GLU* 1.3 69.3 - - - +
498C ILE* 1.3 65.1 + - - +
499C GLY* 3.1 4.2 + - - -
500C LEU* 4.0 30.5 + - + -
507C ARG 3.6 0.2 - - - +
508C VAL* 4.6 0.4 - - - -
509C THR* 2.8 35.0 + - - +
511C VAL* 4.1 8.9 - - + +
560C ILE* 5.5 1.3 - - + -
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Residues in contact with ILE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473C LEU* 5.0 0.9 - - - +
476C ASP 5.2 0.7 - - - +
477C ARG* 3.0 68.6 + - + +
479C VAL* 4.5 17.7 - - + -
496C GLU* 4.5 7.2 - - + +
497C ALA* 1.3 69.5 - - - +
499C GLY* 1.3 67.0 + - - +
505C PRO 3.9 15.0 - - - +
506C ASN* 5.3 2.0 - - - -
507C ARG 3.9 6.7 - - - +
508C VAL* 4.6 18.8 - - + +
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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