Contacts of the helix formed by residues 436 - 447 (chain B) in PDB entry 6FQS
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 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B VAL* 3.5 3.2 + - - +
435B GLU* 1.3 73.6 - - - +
437B ASP* 1.3 70.0 + - - +
438B SER 3.2 3.1 - - - -
439B ALA* 3.1 7.9 + - - +
440B GLY* 3.0 19.6 + - - -
456B PRO* 4.2 3.7 - - - +
457B LEU 3.4 13.6 + - - -
458B ARG 5.4 0.4 + - - -
123C PTR 3.5 25.8 - - - -
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Residues in contact with ASP 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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417B LYS* 6.2 1.1 - - + -
436B GLY* 1.3 71.0 - - - +
438B SER* 1.3 52.7 + - - +
440B GLY* 3.3 2.4 - - - -
441B GLY* 2.5 30.3 + - - -
456B PRO* 3.4 27.1 - - + +
457B LEU 3.6 14.2 - - - +
458B ARG* 3.2 32.5 + - - -
123C PTR 4.3 11.6 + - - -
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Residues in contact with SER 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B GLY 3.2 0.4 - - - -
437B ASP* 1.3 78.9 - - - +
439B ALA* 1.3 60.6 + - - +
441B GLY* 3.4 10.8 - - - +
442B SER* 2.9 22.3 + - - -
584B GLY 5.3 0.9 - - - +
109C ASN* 4.2 5.5 + - - -
118C ALA 4.4 1.9 + - - -
119C ALA* 3.2 44.2 + - - +
120C ALA 4.3 1.3 - - - -
123C PTR 4.0 22.2 - - - +
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Residues in contact with ALA 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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434B VAL* 4.0 5.1 - - + +
435B GLU 3.3 19.3 - - - +
436B GLY* 3.1 14.5 + - - +
438B SER* 1.3 77.4 - - - +
440B GLY* 1.4 55.9 + - - +
442B SER* 2.5 20.5 + - - -
443B THR* 3.2 10.6 - - - +
506B MET* 5.3 0.2 - - - +
583B LEU* 3.5 32.2 - - + +
584B GLY* 4.3 9.2 - - - +
591B LEU* 3.4 6.9 - - - +
123C PTR 4.2 7.6 - - + -
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Residues in contact with GLY 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B VAL* 3.6 21.8 - - - +
436B GLY 3.0 11.2 + - - -
437B ASP 3.3 3.6 - - - -
439B ALA* 1.4 71.0 - - - +
441B GLY* 1.3 63.2 + - - +
442B SER 3.3 0.9 - - - -
443B THR* 2.5 33.5 + - - -
444B LYS* 3.6 4.5 + - - +
454B ILE* 3.8 14.5 - - - +
456B PRO* 5.4 1.1 - - - -
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B ASP 2.5 21.4 + - - -
438B SER* 3.4 10.9 - - - -
439B ALA 3.3 1.4 - - - -
440B GLY* 1.3 71.4 - - - +
442B SER* 1.3 66.9 + - - +
444B LYS* 3.6 13.8 + - - +
445B SER* 4.3 1.6 + - - -
109C ASN* 3.4 15.2 + - - -
116C ASP* 5.4 1.9 - - - +
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Residues in contact with SER 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 SER 2.9 12.7 + - - -
439B ALA* 2.5 26.3 + - - -
441B GLY* 1.3 72.1 - - - +
443B THR* 1.3 51.4 + - - -
444B LYS 2.7 13.3 + - - -
445B SER* 2.7 26.7 + - - -
584B GLY 5.0 2.6 + - - -
586B MET 4.3 6.4 + - - -
588B ALA* 3.2 17.9 - - - +
591B LEU* 3.2 15.4 - - - +
109C ASN* 3.6 28.3 - - - +
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Residues in contact with THR 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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434B VAL* 5.2 0.4 - - + -
439B ALA 3.2 21.1 - - - +
440B GLY* 2.5 26.7 + - - -
442B SER* 1.3 72.3 - - - +
444B LYS* 1.3 51.3 + - - +
446B GLY* 2.8 6.6 + - - +
447B ARG* 2.2 39.0 + - - +
454B ILE* 3.5 18.4 - - - +
506B MET* 4.0 15.5 - - + -
588B ALA* 4.6 3.8 - - - -
591B LEU* 3.7 11.8 - - + +
596B MET* 3.3 31.0 - - + -
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Residues in contact with LYS 444 (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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419B ALA* 5.4 6.3 - - + -
440B GLY 4.3 4.9 - - - +
441B GLY* 3.6 13.4 + - - +
442B SER 2.7 5.9 + - - -
443B THR* 1.3 79.2 + - - +
445B SER* 1.3 62.3 + - - +
446B GLY 3.3 0.2 + - - -
447B ARG* 3.4 38.8 + - - +
449B SER* 5.6 1.9 - - - -
454B ILE* 5.3 2.5 - - + -
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Residues in contact with SER 445 (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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441B GLY 4.3 1.4 + - - -
442B SER* 2.7 24.2 + - - -
444B LYS* 1.3 75.0 - - - +
446B GLY* 1.3 58.0 + - - +
447B ARG 4.4 1.9 - - - +
588B ALA* 2.9 20.1 - - - +
109C ASN* 5.1 7.1 + - - -
111C GLY 5.8 2.5 - - - -
112C SER* 5.7 9.9 - - - -
297C SER* 6.0 0.2 - - - -
298C LEU* 3.6 27.5 + - - +
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Residues in contact with GLY 446 (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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442B SER 3.6 0.2 + - - -
443B THR 2.8 12.5 + - - -
445B SER* 1.3 77.9 + - - +
447B ARG* 1.3 64.9 + - - +
588B ALA* 3.9 21.3 - - - +
592B TRP* 3.4 28.3 - - - -
298C LEU* 4.1 15.2 - - - +
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Residues in contact with ARG 447 (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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419B ALA* 3.8 23.0 + - - +
420B ASP 4.2 10.1 + - - -
421B CYS 4.8 0.8 - - - +
443B THR* 2.2 26.9 + - - +
444B LYS* 3.4 39.7 + - - +
445B SER 4.4 1.7 - - - +
446B GLY 1.3 70.9 - - - +
448B ASP* 1.3 61.1 + - - +
449B SER* 3.1 35.1 + - - +
452B GLN* 1.8 49.3 + - + +
453B ALA* 3.8 2.6 - - - +
454B ILE* 3.6 21.6 - - + +
592B TRP* 3.6 10.2 - - - +
596B MET* 3.9 15.0 - - + -
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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