Contacts of the helix formed by residues 493 - 503 (chain B) in PDB entry 4G84
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 ASP 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489B VAL* 4.1 10.1 - - + -
490B ARG* 2.9 57.6 + - - +
492B GLU* 1.3 82.4 - - - +
494B LEU* 1.3 53.1 + - - +
495B VAL 3.3 2.2 - - - -
496B GLU* 3.1 11.1 + - + +
497B GLU* 2.7 35.3 + - + +
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Residues in contact with LEU 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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427B LEU* 4.0 31.0 - - + -
431B LEU* 4.2 12.6 - - + -
464B ALA* 4.7 4.5 - - + -
476B ILE* 4.1 33.2 - - + -
478B LEU* 4.3 20.0 - - + -
489B VAL* 4.0 13.9 - - + -
490B ARG 3.3 5.0 + - - +
491B ARG* 3.1 20.8 + - - +
493B ASP* 1.3 77.7 - - - +
495B VAL* 1.3 65.3 + - + +
497B GLU* 3.2 1.2 + - - +
498B ILE* 2.9 50.5 + - + +
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Residues in contact with VAL 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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430B GLU* 5.3 4.0 - - + +
431B LEU* 4.4 14.8 - - + -
434B ALA* 3.8 28.9 - - + -
436B ILE* 3.6 22.5 - - + +
491B ARG 4.7 2.0 + - - +
492B GLU 4.9 5.3 + - - +
493B ASP 3.3 0.4 - - - -
494B LEU* 1.3 78.0 - - + +
496B GLU* 1.3 58.8 + - - +
498B ILE 3.3 0.2 + - - -
499B LYS* 3.0 51.4 + - - +
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Residues in contact with GLU 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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492B GLU 5.4 1.0 + - - +
493B ASP* 3.1 12.7 + - + +
495B VAL* 1.3 79.4 - - - +
497B GLU* 1.3 58.7 + - - +
499B LYS* 3.3 10.9 + - - +
500B ARG* 2.9 31.4 + - - +
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Residues in contact with GLU 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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478B LEU* 3.9 14.8 - - + -
489B VAL* 4.1 25.4 - - + -
493B ASP* 2.7 22.9 + - + +
494B LEU* 3.7 3.8 - - - +
496B GLU* 1.3 73.8 - - - +
498B ILE* 1.3 61.0 + - - +
500B ARG* 2.6 33.4 + - - +
501B ARG* 2.5 58.5 + - - +
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Residues in contact with ILE 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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410B GLN* 4.2 27.6 - - + +
411B VAL* 3.8 29.8 - - + -
431B LEU* 4.2 6.5 - - + -
436B ILE* 4.0 21.1 - - + -
462B LEU* 4.1 24.7 - - + -
478B LEU* 4.4 4.7 - - + -
494B LEU* 2.9 45.1 + - + +
495B VAL 3.7 3.4 - - - +
497B GLU* 1.3 75.6 - - - +
499B LYS* 1.3 66.7 + - - +
501B ARG* 3.1 10.7 + - - +
502B THR* 3.0 18.5 + - - +
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Residues in contact with LYS 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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434B ALA 4.4 14.5 + - - -
436B ILE* 4.6 7.4 - - + -
495B VAL* 3.0 39.8 + - + +
496B GLU* 3.5 12.3 - - - +
498B ILE* 1.3 77.1 - - - +
500B ARG* 1.3 62.0 + - - +
502B THR* 3.4 6.2 + - - -
503B GLY 3.1 18.2 + - - -
504B GLN* 3.3 55.8 + - + +
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Residues in contact with ARG 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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496B GLU 2.9 17.1 + - - +
497B GLU* 2.6 41.5 + - - +
499B LYS* 1.3 75.4 - - - +
501B ARG* 1.3 79.1 + - - +
502B THR 3.1 1.6 + - - -
503B GLY* 3.3 11.9 + - - -
504B GLN 5.5 0.2 - - - +
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Residues in contact with ARG 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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461B PRO* 6.0 0.9 - - - +
462B LEU* 3.8 34.1 - - + +
478B LEU* 4.1 22.9 + - - +
480B SER* 4.9 10.3 - - - +
485B GLU 5.7 0.4 + - - -
487B VAL* 3.7 23.6 - - - +
497B GLU* 2.5 46.3 + - - +
498B ILE 3.1 5.7 + - - +
500B ARG* 1.3 94.2 - - - +
502B THR* 1.3 61.5 + - - +
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Residues in contact with THR 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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410B GLN* 2.6 49.6 + - + +
461B PRO* 4.2 21.1 - - + -
462B LEU* 4.4 11.9 - - + -
498B ILE* 3.0 13.4 + - + +
499B LYS* 3.6 4.2 + - - -
500B ARG 3.1 0.2 - - - -
501B ARG* 1.3 82.4 - - - +
503B GLY* 1.3 68.4 + - - +
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Residues in contact with GLY 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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410B GLN* 5.7 0.3 + - - -
499B LYS 3.1 7.1 + - - -
500B ARG 3.3 9.7 + - - -
501B ARG 3.6 0.2 - - - -
502B THR* 1.3 83.2 + - - +
504B GLN* 1.3 60.2 + - - +
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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