Contacts of the helix formed by residues 492 - 504 (chain B) in PDB entry 1EQR
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 ASN 492 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ASN* 5.2 8.0 - - - +
490B ILE* 3.3 5.0 - - + +
491B HIS* 1.3 87.2 + - + +
493B GLY* 1.3 62.7 + - - +
494B ASP* 2.8 34.3 + - - +
495B MET* 2.8 35.7 + - + +
496B GLN 3.2 4.9 + - - -
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Residues in contact with GLY 493 (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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103A ASN* 6.0 0.2 - - - +
491B HIS 3.5 5.5 + - - -
492B ASN* 1.3 69.5 + - - +
494B ASP* 1.3 65.9 + - - +
496B GLN* 3.2 10.6 + - - +
497B GLN* 3.1 26.8 + - - +
521B LEU* 6.4 2.0 - - - -
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Residues in contact with ASP 494 (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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459B ALA* 5.0 8.1 - - + -
492B ASN* 2.8 23.2 + - - +
493B GLY* 1.3 73.1 - - - +
495B MET* 1.3 63.0 + - - +
497B GLN* 3.3 8.4 + - - +
498B THR* 3.1 25.8 + - - -
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Residues in contact with MET 495 (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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454B PRO* 3.6 30.3 - - + -
457B MET 5.5 2.2 - - - +
458B THR 4.3 1.1 - - - -
459B ALA* 3.2 45.1 - - + +
462B LEU* 3.3 28.0 - - + -
490B ILE* 4.0 16.4 - - + -
492B ASN* 2.8 27.8 + - + +
494B ASP* 1.3 75.5 - - - +
496B GLN* 1.3 63.5 + - - +
498B THR* 3.3 5.9 + - - -
499B VAL* 3.0 20.5 + - - +
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Residues in contact with GLN 496 (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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450B PRO 3.1 22.6 + - - -
451B PHE* 3.0 37.3 - - + -
490B ILE* 3.6 32.4 - - + +
492B ASN 3.2 4.3 + - - +
493B GLY* 3.2 12.5 + - - +
495B MET* 1.3 78.3 - - - +
497B GLN* 1.3 63.0 + - + +
499B VAL* 3.3 4.0 + - - +
500B PHE* 3.1 54.7 + - + -
518B LEU* 4.3 6.5 - - + -
521B LEU* 5.0 6.2 - - + +
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Residues in contact with GLN 497 (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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493B GLY 3.1 14.9 + - - +
494B ASP* 3.4 11.9 - - - +
496B GLN* 1.3 75.2 - - + +
498B THR* 1.3 60.6 + - - +
500B PHE* 3.3 9.6 + - - +
501B GLY* 2.8 25.8 + - - -
507B GLU* 5.6 6.5 - - - +
510B GLN* 3.1 33.3 + - - +
518B LEU* 5.8 0.2 - - - +
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Residues in contact with THR 498 (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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459B ALA* 3.3 36.2 + - - +
463B LYS* 3.6 33.3 + - + +
494B ASP 3.1 13.7 + - - -
495B MET* 3.3 17.2 + - + -
497B GLN* 1.3 72.4 - - - +
499B VAL* 1.3 67.6 + - - +
501B GLY* 3.1 2.6 + - - +
502B ILE* 2.9 32.1 + - + +
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Residues in contact with VAL 499 (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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435B MET* 4.3 20.4 - - + -
436B PHE* 4.6 9.6 - - + -
450B PRO* 3.4 24.2 - - + +
452B THR 4.4 0.9 - - - +
462B LEU* 4.6 2.9 - - + -
490B ILE* 3.5 23.1 - - + -
495B MET* 3.0 24.4 + - - +
496B GLN* 3.5 9.2 - - - +
498B THR* 1.3 75.9 - - - +
500B PHE* 1.3 54.5 + - - +
502B ILE* 2.9 14.9 + - - +
503B LEU* 2.8 52.0 + - + +
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Residues in contact with PHE 500 (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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450B PRO* 4.0 13.2 - - + -
451B PHE* 4.2 3.1 - + - -
496B GLN* 3.1 37.9 + - + -
497B GLN* 3.5 14.1 - - - +
499B VAL* 1.3 80.5 - - + +
501B GLY* 1.3 63.5 + - - +
503B LEU* 3.2 4.2 + - - -
504B GLY* 3.0 18.7 + - - -
505B ILE* 3.1 34.1 + - + +
510B GLN* 3.1 45.5 - - + +
514B PHE* 3.3 42.0 - + - -
518B LEU* 3.8 21.3 - - + -
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Residues in contact with GLY 501 (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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463B LYS* 6.1 2.9 - - - -
497B GLN 2.8 13.8 + - - -
498B THR* 3.6 4.3 - - - -
499B VAL 3.1 0.4 - - - -
500B PHE* 1.3 75.8 - - - +
502B ILE* 1.3 64.6 + - - +
504B GLY* 3.2 11.7 + - - -
505B ILE 5.3 0.4 - - - -
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Residues in contact with ILE 502 (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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436B PHE* 3.7 18.4 - - + -
443B GLY 5.5 0.3 - - - -
444B LEU* 3.5 42.3 + - + +
462B LEU* 3.5 55.2 - - + +
463B LYS* 4.4 9.2 - - + +
466B PRO* 3.7 11.4 - - + -
498B THR* 2.9 25.2 + - + +
499B VAL 2.9 7.0 + - - +
501B GLY* 1.3 77.3 - - - +
503B LEU* 1.3 61.2 + - - +
504B GLY 3.3 1.4 + - - -
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Residues in contact with LEU 503 (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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436B PHE* 3.5 33.9 - - + -
444B LEU 3.9 13.8 - - - +
445B THR* 3.9 8.7 - - - +
446B ALA* 3.7 26.5 - - + +
450B PRO* 3.8 23.3 - - + -
499B VAL* 2.8 35.8 + - + +
500B PHE* 3.5 7.9 - - - +
501B GLY 3.1 0.2 - - - -
502B ILE* 1.3 79.1 - - + +
504B GLY* 1.3 57.7 + - - +
505B ILE* 3.1 23.1 + - + +
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Residues in contact with GLY 504 (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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500B PHE 3.0 5.3 + - - -
501B GLY 3.2 11.0 + - - -
502B ILE 3.3 2.0 + - - -
503B LEU* 1.3 76.8 - - - +
505B ILE* 1.3 58.6 + - - +
506B ASN* 3.2 9.7 + - - +
509B GLU* 3.7 8.8 - - - +
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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