Contacts of the helix formed by residues 435 - 443 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432D THR* 2.8 24.7 + - - +
433D LYS 3.6 0.8 - - - -
434D SER* 1.3 78.0 - - - +
436D ARG* 1.3 64.6 - - - +
437D SER 3.3 2.9 - - - -
438D ALA* 3.0 7.2 + - - +
439D HIS* 2.9 38.4 + - - -
459D THR* 4.3 7.2 - - - -
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Residues in contact with ARG 436 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434D SER* 3.0 35.7 + - - +
435D GLY* 1.3 76.5 - - - +
437D SER* 1.3 56.8 + - - +
439D HIS* 3.2 17.1 + - + +
440D GLN* 2.9 37.7 + - - +
1003D SO4 4.2 8.8 + - - +
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Residues in contact with SER 437 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409D THR* 4.8 6.9 - - - +
413D ALA* 5.3 0.2 - - - +
430D VAL* 3.5 17.1 - - - +
431D LEU 4.9 0.4 - - - -
432D THR* 4.3 2.9 - - - -
436D ARG* 1.3 76.9 - - - +
438D ALA* 1.3 60.9 + - - +
440D GLN* 3.6 11.8 + - - +
441D VAL* 3.3 24.9 + - - +
512D LEU* 5.2 2.1 - - - +
522D THR* 3.0 37.7 + - - +
1003D SO4 3.0 22.6 + - - -
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Residues in contact with ALA 438 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D VAL* 4.0 20.3 - - + +
432D THR* 4.4 4.5 + - + -
435D GLY* 3.0 12.7 + - - +
437D SER* 1.3 77.2 - - - +
439D HIS* 1.3 59.3 + - + +
440D GLN 3.2 0.2 - - - -
441D VAL* 3.3 4.6 + - - +
442D ALA* 3.0 27.7 + - - +
450D ILE* 4.4 5.1 - - + +
452D ALA* 3.9 25.1 - - + -
469D ILE* 3.5 18.9 - - + +
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Residues in contact with HIS 439 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266D LYS* 4.0 18.6 + - - -
321D GLY 4.9 3.7 - - - +
434D SER 4.4 3.8 - - - -
435D GLY* 3.0 37.4 + - - -
436D ARG* 3.2 18.0 + - + +
438D ALA* 1.3 76.1 - - + +
440D GLN* 1.3 62.7 + - - +
442D ALA* 3.2 9.2 + - - +
443D ARG* 3.1 24.3 + - - +
459D THR 5.6 1.0 + - - -
462D GLN* 5.2 1.2 + - - +
463D ALA* 4.8 10.8 + - + +
466D TYR* 3.3 61.1 + + + +
469D ILE* 4.0 8.7 - - + -
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Residues in contact with GLN 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407D ASP* 4.4 1.8 + - - -
409D THR* 3.5 32.0 - - + +
410D GLU* 3.2 36.2 + - + +
413D ALA* 4.2 13.2 - - + -
436D ARG* 2.9 23.2 + - - +
437D SER* 3.6 8.6 - - - +
439D HIS* 1.3 79.0 - - - +
441D VAL* 1.3 59.9 + - - +
443D ARG* 3.7 11.6 + - + +
444D TYR* 3.3 27.8 - - + -
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Residues in contact with VAL 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413D ALA* 3.9 18.6 - - + +
416D ALA* 5.1 0.2 - - + -
417D VAL* 3.7 20.8 - - + +
428D ILE* 4.0 19.3 - - + -
430D VAL* 4.2 8.1 - - + -
437D SER* 3.3 16.4 - - - +
438D ALA 3.3 6.6 + - - +
439D HIS 3.3 0.2 - - - -
440D GLN* 1.3 74.3 - - - +
442D ALA* 1.3 65.4 + - - +
443D ARG 3.2 0.4 - - - -
444D TYR* 3.2 18.0 + - - +
446D PRO* 3.6 9.2 - - - +
450D ILE* 3.7 18.2 - - + -
512D LEU* 3.6 28.5 - - + -
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Residues in contact with ALA 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D ALA 3.0 16.9 + - - +
439D HIS* 3.2 7.6 + - - +
441D VAL* 1.3 78.2 - - - +
443D ARG* 1.3 56.6 + - - +
444D TYR 3.1 0.7 - - - -
445D ARG* 3.0 30.9 + - - -
446D PRO* 4.5 0.9 - - - -
450D ILE* 3.6 12.1 - - + +
466D TYR* 4.4 10.3 - - + -
467D ARG 4.0 12.7 - - - +
469D ILE* 3.7 26.0 - - + -
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Residues in contact with ARG 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318D ASN 4.2 4.2 - - - +
319D ARG 2.9 26.6 + - - -
320D ALA* 4.0 9.0 + - - +
321D GLY* 3.6 29.8 - - - +
398D LEU* 3.3 33.9 + - - +
401D LEU* 4.2 19.2 + - - +
439D HIS 3.1 13.8 + - - +
440D GLN* 3.7 15.9 - - - +
441D VAL 3.2 1.0 - - - -
442D ALA* 1.3 77.0 - - - +
444D TYR* 1.3 93.5 + - + +
445D ARG* 3.3 6.2 + - - +
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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