Contacts of the helix formed by residues 436 - 447 (chain u) in PDB entry 6QX2
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 u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434u VAL* 3.4 1.9 - - - +
435u GLU* 1.3 79.3 - - - +
437u ASP* 1.3 57.2 + - - -
438u SER* 3.2 4.2 + - - -
439u ALA* 3.3 4.1 + - - +
440u GLY* 2.8 30.7 + - - -
456u PRO* 3.7 8.1 - - - +
457u LEU 3.4 11.2 - - - -
2009w G 4.0 14.7 + - - -
2010w G 3.6 8.5 - - - -
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Residues in contact with ASP 437 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109r ASN* 3.4 6.3 + - - -
119r ALA* 5.5 1.1 - - - -
417u LYS* 5.9 1.6 - - - +
436u GLY* 1.3 69.2 - - - -
438u SER* 1.3 62.4 + - - +
440u GLY* 3.7 5.6 - - - +
441u GLY* 3.0 20.0 + - - +
456u PRO* 3.9 17.4 - - - +
457u LEU 5.0 1.7 - - - +
458u ARG* 6.0 0.5 - - - +
2010w G 2.7 34.6 + - - +
2011w C 3.2 27.1 + - - -
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Residues in contact with SER 438 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109r ASN* 2.9 24.7 + - - +
119r ALA* 3.7 23.0 - - - +
120r ALA 5.3 0.4 - - - -
123r TYR* 3.2 34.0 - - - -
436u GLY* 3.9 3.8 - - - -
437u ASP* 1.3 72.3 - - - +
439u ALA* 1.3 65.0 + - - +
442u SER* 3.5 10.0 + - - -
584u GLY* 3.7 5.4 + - - -
2009w G 2.7 26.2 + - - -
2010w G 3.6 5.8 + - - -
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Residues in contact with ALA 439 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434u VAL* 4.0 20.9 - - + -
435u GLU* 4.5 7.6 - - + +
436u GLY 3.3 6.4 + - - +
438u SER* 1.3 80.3 + - - +
440u GLY* 1.3 62.4 + - - +
441u GLY 3.3 0.3 + - - -
442u SER* 3.3 2.3 + - - -
443u THR* 2.6 33.3 + - - +
506u MET 5.8 0.2 - - - +
508u ASP* 5.1 3.6 - - - +
583u LEU* 3.9 27.4 - - + +
584u GLY* 4.0 9.2 - - - +
2009w G 5.6 0.2 - - - +
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Residues in contact with GLY 440 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434u VAL* 3.8 15.8 - - - +
436u GLY 2.8 21.2 + - - -
437u ASP* 3.7 4.5 - - - -
438u SER 3.4 0.2 - - - -
439u ALA* 1.3 72.4 - - - +
441u GLY* 1.3 55.5 + - - +
443u THR* 3.4 2.4 + - - -
444u LYS* 2.9 39.8 + - - +
454u ILE* 4.2 3.7 - - - +
456u PRO* 4.2 13.7 - - - -
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Residues in contact with GLY 441 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109r ASN* 3.4 19.5 - - - -
116r ASP* 4.8 16.3 - - - -
437u ASP 3.0 12.0 + - - -
440u GLY* 1.3 70.3 - - - +
442u SER* 1.3 65.7 + - - +
444u LYS* 3.3 10.8 + - - +
445u SER* 3.1 25.6 + - - -
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Residues in contact with SER 442 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109r ASN* 3.0 31.4 + - - +
438u SER 3.5 3.8 + - - -
439u ALA 3.3 8.0 + - - -
441u GLY* 1.3 75.6 - - - +
443u THR* 1.3 56.4 - - - +
445u SER* 3.6 1.1 + - - -
446u GLY* 3.2 21.1 + - - -
583u LEU 3.6 17.9 + - - -
586u MET 3.5 16.8 + - - -
588u ALA* 3.2 24.3 - - - +
591u LEU* 3.8 12.3 - - - +
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Residues in contact with THR 443 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432u PHE* 4.6 1.8 - - + -
434u VAL* 4.0 6.0 - - + +
439u ALA* 2.6 25.9 + - - +
440u GLY* 3.5 5.8 - - - -
442u SER* 1.3 74.2 - - - +
444u LYS* 1.3 59.6 + - - +
446u GLY* 3.1 1.4 + - - -
447u ARG* 2.9 32.6 + - - +
454u ILE* 3.4 29.8 - - + -
506u MET* 3.7 22.6 - - + +
591u LEU* 3.6 16.3 - - - +
596u MET* 3.6 21.1 - - + +
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Residues in contact with LYS 444 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116r ASP* 4.1 22.0 - - - +
417u LYS 5.9 1.6 - - - +
419u ALA* 3.8 28.3 - - + -
440u GLY* 2.9 26.1 + - - +
441u GLY* 3.3 6.0 + - - +
443u THR* 1.3 75.0 - - - +
445u SER* 1.3 57.1 + - - +
447u ARG* 3.1 25.8 + - - +
449u SER* 5.7 0.3 - - - -
454u ILE* 3.5 24.7 - - + -
456u PRO* 5.6 5.2 - - + -
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Residues in contact with SER 445 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111r GLY 5.3 1.2 + - - -
112r SER* 4.1 21.0 - - - -
297r SER* 4.7 4.5 - - - -
298r LEU* 4.2 29.8 + - - +
441u GLY 3.1 12.8 + - - -
442u SER* 3.7 3.8 - - - -
444u LYS* 1.3 77.9 - - - +
446u GLY* 1.3 61.1 + - - +
447u ARG 3.5 4.9 + - - +
588u ALA* 3.5 20.9 - - - -
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Residues in contact with GLY 446 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297r SER* 5.9 1.2 - - - -
298r LEU* 5.4 2.2 - - - -
442u SER 3.2 7.9 + - - -
443u THR 3.1 6.0 + - - -
445u SER* 1.3 78.7 - - - +
447u ARG* 1.3 63.9 + - - +
588u ALA* 3.6 24.7 - - - +
591u LEU* 5.8 0.7 - - - -
592u TRP* 3.2 30.3 - - - +
596u MET* 4.5 4.7 - - - -
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Residues in contact with ARG 447 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296r THR 5.2 2.1 - - - +
297r SER* 4.8 11.3 - - - -
419u ALA* 2.9 43.1 + - - +
420u ASP 3.3 17.8 + - - -
421u CYS 4.1 0.4 - - - +
443u THR 2.9 13.0 + - - +
444u LYS* 3.1 26.9 + - - +
445u SER 3.3 5.2 - - - +
446u GLY* 1.3 81.7 - - - +
448u ASP* 1.3 57.1 + - - +
449u SER* 3.6 33.7 + - - +
452u GLN* 2.8 50.5 + - + +
453u ALA* 3.9 0.6 - - - +
454u ILE* 3.5 13.4 - - + +
592u TRP* 4.2 1.6 - - - -
596u MET* 3.6 14.3 - - + -
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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