Contacts of the helix formed by residues 435 - 443 (chain B) in PDB entry 4QGC
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 GLY 435 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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432B THR* 2.8 25.0 + - - +
433B LYS 3.5 1.2 - - - -
434B SER* 1.3 78.2 - - - +
436B ARG* 1.3 63.9 + - - +
437B SER 3.3 2.9 - - - -
438B ALA* 3.1 5.4 + - - +
439B HIS* 3.0 40.3 + - - -
459B THR* 4.3 8.3 - - - +
463B ALA* 6.4 0.9 - - - -
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Residues in contact with ARG 436 (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 GLU* 5.0 1.2 + - - -
434B SER* 3.3 18.2 + - - +
435B GLY* 1.3 77.9 - - - +
437B SER* 1.3 57.9 + - - +
439B HIS* 3.1 18.8 + - - +
440B GLN* 3.0 74.2 + - - +
443B ARG* 6.0 1.8 - - - +
1002B SO4 3.3 6.6 + - - +
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Residues in contact with SER 437 (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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409B THR* 4.6 6.2 - - - +
413B ALA* 5.3 0.5 - - - +
430B VAL* 3.6 9.7 - - - +
432B THR* 3.2 15.4 + - - -
436B ARG* 1.3 75.6 - - - +
438B ALA* 1.3 62.9 + - - +
440B GLN* 3.4 14.9 + - - +
441B VAL* 3.3 25.6 + - - +
512B LEU* 6.5 0.2 - - - -
522B THR* 3.3 39.1 + - - +
1002B SO4 3.0 18.7 + - - -
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B VAL* 4.0 18.8 - - + +
432B THR* 4.3 5.8 - - + -
435B GLY* 3.1 9.9 + - - +
437B SER* 1.3 77.7 + - - +
439B HIS* 1.3 60.4 + - + +
441B VAL* 3.3 7.4 + - - +
442B ALA* 3.0 22.5 + - - +
450B ILE* 4.4 4.9 - - + +
452B ALA* 3.9 28.5 - - + -
463B ALA* 6.4 0.4 - - + -
469B ILE* 3.4 20.4 - - + +
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Residues in contact with HIS 439 (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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266B LYS* 3.8 17.0 - - - -
321B GLY 5.1 3.8 - - - +
434B SER 4.5 4.3 - - - -
435B GLY* 3.0 40.1 + - - -
436B ARG* 3.1 21.5 + - - +
438B ALA* 1.3 77.9 - - + +
440B GLN* 1.3 56.2 + - - +
442B ALA* 3.2 4.5 + - - +
443B ARG* 3.1 26.9 + - - +
459B THR 5.5 1.0 + - - -
462B GLN* 5.0 1.5 + - + -
463B ALA* 4.6 11.8 + - + +
466B TYR* 3.2 61.2 + + + -
469B ILE* 3.9 12.8 - - + -
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Residues in contact with GLN 440 (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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407B ASP* 4.0 11.3 + - - -
409B THR* 3.4 29.2 - - + +
410B GLU* 2.8 32.0 + - - +
413B ALA* 4.2 9.2 - - + -
436B ARG* 3.0 62.8 + - - +
437B SER* 3.7 9.6 - - - +
438B ALA 3.3 0.2 - - - -
439B HIS* 1.3 76.9 - - - +
441B VAL* 1.3 59.5 + - - +
443B ARG* 3.7 9.8 - - - +
444B TYR* 3.1 28.2 - - - -
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Residues in contact with VAL 441 (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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413B ALA* 4.1 18.2 - - + +
416B ALA* 5.3 0.2 - - + -
417B VAL* 3.8 18.8 - - + +
428B ILE* 4.0 20.4 - - + -
430B VAL* 4.3 7.2 - - + -
437B SER 3.3 15.2 + - - +
438B ALA* 3.7 7.4 - - - +
439B HIS 3.2 0.6 - - - -
440B GLN* 1.3 76.5 - - - +
442B ALA* 1.3 64.2 + - - +
443B ARG 3.2 0.2 - - - -
444B TYR* 3.1 17.4 + - - +
446B PRO* 3.6 9.5 - - - +
450B ILE* 3.7 19.7 - - + -
512B LEU* 3.7 28.0 - - + -
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Residues in contact with ALA 442 (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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438B ALA 3.0 16.8 + - - +
439B HIS* 3.2 7.2 + - - +
441B VAL* 1.3 75.7 - - - +
443B ARG* 1.3 62.0 + - - +
445B ARG* 2.9 34.3 + - - +
446B PRO* 4.6 1.1 - - - -
450B ILE* 3.5 10.3 - - + +
466B TYR* 4.3 10.8 - - + -
467B ARG 3.9 12.9 - - - +
469B ILE* 3.7 25.8 - - + -
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Residues in contact with ARG 443 (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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318B ASN 4.0 7.4 + - - +
319B ARG* 2.4 30.7 + - - +
320B ALA* 3.2 23.4 + - - +
321B GLY* 3.6 23.6 - - - +
398B LEU* 3.1 30.2 - - + +
402B ALA* 4.7 8.1 - - - +
403B PRO* 3.7 29.3 - - - +
410B GLU* 4.6 6.9 + - - -
436B ARG* 6.0 2.0 - - - +
439B HIS 3.1 11.5 + - - +
440B GLN* 3.7 12.8 - - - +
441B VAL 3.2 0.2 - - - -
442B ALA* 1.3 77.0 - - - +
444B TYR* 1.3 82.3 + - - +
445B ARG* 3.4 9.9 + - - +
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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