Contacts of the helix formed by residues 629 - 644 (chain B) in PDB entry 5QSY
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 GLU 629 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ALA* 3.8 33.3 - - + +
587B GLU* 4.9 2.8 + - - +
627B HIS* 3.8 3.5 - - - +
628B VAL* 1.3 75.5 - - - +
630B SER* 1.3 70.1 + - - +
631B ASP* 3.1 36.5 + - - +
632B VAL* 2.9 23.1 + - + +
633B LEU* 3.3 9.2 + - - +
696B LYS* 4.2 2.0 - - - +
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Residues in contact with SER 630 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628B VAL 3.4 3.8 + - - -
629B GLU* 1.3 74.8 - - - +
631B ASP* 1.3 62.6 + - - +
633B LEU* 3.4 7.1 + - - +
634B GLU* 2.8 34.8 + - - +
696B LYS* 3.5 25.2 + - - +
700B SER* 5.4 1.5 - - - -
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Residues in contact with ASP 631 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B ALA* 4.2 15.2 - - + +
629B GLU* 3.0 25.4 + - - +
630B SER* 1.3 83.3 - - - +
632B VAL* 1.3 62.0 + - - +
634B GLU* 4.1 11.0 - - - +
635B ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 632 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ALA* 3.2 35.9 - - + +
589B VAL* 4.1 7.6 - - + -
590B ALA* 4.8 4.0 - - - +
593B LEU* 4.2 0.2 - - - +
623B VAL* 3.4 34.1 - - + -
627B HIS* 3.5 35.2 - - + +
629B GLU* 2.9 13.4 + - + +
631B ASP* 1.3 73.4 - - - +
633B LEU* 1.3 58.4 + - + +
635B ALA* 3.1 6.9 + - - +
636B CYS* 2.8 41.6 + - - -
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Residues in contact with LEU 633 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B VAL* 3.6 28.0 - - + -
627B HIS* 3.4 26.9 - - + +
628B VAL* 3.7 14.1 - - - +
629B GLU 3.3 10.9 + - - +
630B SER* 3.7 5.6 - - - +
632B VAL* 1.3 75.5 - - - +
634B GLU* 1.3 66.1 + - - +
636B CYS* 3.1 8.7 + - - +
637B SER* 2.9 23.0 + - - -
693B SER 5.7 0.2 - - - +
696B LYS* 3.6 47.6 - - + +
697B ARG* 3.9 9.9 - - + +
700B SER* 3.4 19.7 + - - +
701B PHE* 4.4 1.0 - - - -
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Residues in contact with GLU 634 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630B SER* 2.8 24.1 + - - +
631B ASP* 4.1 10.9 - - - +
633B LEU* 1.3 72.6 - - - +
635B ALA* 1.3 58.7 + - - +
637B SER* 3.1 8.2 + - - -
638B LYS* 2.8 57.9 + - + +
700B SER* 4.5 9.1 - - - +
703B ASN* 6.1 2.9 - - - +
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Residues in contact with ALA 635 (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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590B ALA* 4.2 7.2 - - + +
593B LEU* 3.8 24.7 - - + +
594B GLN* 4.1 17.9 - - - +
631B ASP 3.1 17.3 + - - +
632B VAL 3.1 5.3 + - - +
634B GLU* 1.3 79.8 - - - +
636B CYS* 1.3 52.7 + - - +
638B LYS* 3.5 9.2 + - - +
639B THR* 2.6 37.5 + - - -
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Residues in contact with CYS 636 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B LEU* 3.8 18.2 - - - -
620B ILE* 4.1 21.2 - - + +
623B VAL* 3.8 24.2 - - - -
624B VAL* 4.2 15.5 - - + -
632B VAL* 2.8 22.7 + - - -
633B LEU* 3.5 8.5 - - - +
635B ALA* 1.3 73.5 - - - +
637B SER* 1.3 63.7 + - - +
639B THR* 3.2 6.1 + - - -
640B TYR* 3.2 27.9 + - - -
701B PHE* 4.1 12.1 - - + -
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Residues in contact with SER 637 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633B LEU 2.9 12.7 + - - -
634B GLU* 3.4 9.9 - - - -
636B CYS* 1.3 76.6 - - - +
638B LYS* 1.3 57.2 + - - +
640B TYR* 3.6 0.3 - - - +
641B SER* 2.9 15.0 + - - -
700B SER 3.6 21.9 + - - -
701B PHE* 3.7 26.9 - - - -
704B ALA* 4.0 9.9 - - - +
705B HIS* 2.9 36.4 + - - -
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Residues in contact with LYS 638 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B GLN* 6.0 1.6 - - - +
634B GLU* 2.8 48.9 + - + +
635B ALA* 3.8 8.7 - - - +
636B CYS 3.4 0.4 - - - -
637B SER* 1.3 73.7 - - - +
639B THR* 1.3 60.7 + - - +
641B SER* 3.5 10.8 + - - -
642B ILE* 3.3 30.7 + - + +
703B ASN* 6.0 2.0 - - - +
704B ALA* 5.9 0.7 - - - -
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Residues in contact with THR 639 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B LEU* 3.5 25.5 + - + +
596B PRO* 3.7 31.2 - - + -
616B LEU* 5.0 0.9 - - + -
620B ILE* 3.6 26.0 - - + -
635B ALA 2.6 22.6 + - - -
636B CYS* 3.6 6.1 - - - -
637B SER 3.2 0.6 - - - -
638B LYS* 1.3 74.7 - - - +
640B TYR* 1.3 61.6 - - - +
642B ILE* 3.1 9.1 + - - +
643B LEU* 2.9 38.3 + - + +
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Residues in contact with TYR 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617B LEU* 3.8 34.0 + - + +
620B ILE* 3.7 26.4 - - + +
621B LYS* 5.3 2.3 + - - +
636B CYS 3.2 17.2 + - - +
637B SER 3.6 9.4 - - - +
639B THR* 1.3 75.9 - - - +
641B SER* 1.3 62.1 + - - +
643B LEU* 4.4 3.5 - - - +
644B CYS* 3.0 29.9 + - - -
654B VAL* 3.7 21.1 - - + -
657B ALA* 3.8 23.7 + - - +
658B ARG* 3.9 29.6 - - + -
661B LEU* 3.8 21.7 - - + +
701B PHE* 3.8 14.4 - + + -
705B HIS* 3.6 16.2 - + + +
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Residues in contact with SER 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B SER 2.9 18.0 + - - -
638B LYS* 3.6 14.4 - - - -
639B THR 3.3 0.4 - - - -
640B TYR* 1.3 73.7 - - - +
642B ILE* 1.3 60.1 + - - +
644B CYS* 3.5 16.1 - - - +
645B SER* 4.9 0.7 - - - -
704B ALA* 4.4 17.2 + - - +
705B HIS* 3.5 15.1 - - - -
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Residues in contact with ILE 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B LEU 6.1 0.7 - - - +
596B PRO* 4.1 18.4 - - + +
597B GLN* 3.3 38.1 - - + +
601B LEU* 3.5 22.2 - - + +
638B LYS* 3.3 20.5 + - + +
639B THR* 3.1 10.9 + - - +
641B SER* 1.3 75.8 - - - +
643B LEU* 1.3 69.1 + - + +
645B SER* 3.5 20.2 + - - +
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Residues in contact with LEU 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B PRO* 4.5 19.1 - - + -
599B PHE* 5.6 0.2 - - + -
601B LEU* 4.1 23.1 - - + -
604B TYR* 5.1 2.9 - - + -
613B LEU* 4.2 14.8 - - + -
616B LEU* 4.2 17.3 - - + -
617B LEU* 3.7 27.6 - - + -
620B ILE* 4.5 2.9 - - + -
639B THR* 2.9 34.6 + - + +
640B TYR* 3.9 3.8 - - - +
642B ILE* 1.3 75.6 - - + +
644B CYS* 1.3 52.3 + - - +
645B SER* 2.7 25.8 + - - -
650B ILE* 4.4 8.7 - - + +
651B GLN* 4.6 2.1 - - - -
654B VAL* 3.6 28.2 - - + +
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Residues in contact with CYS 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B TYR* 3.0 19.7 + - - +
641B SER* 3.5 14.4 - - - +
643B LEU* 1.3 69.3 - - - +
645B SER* 1.3 62.6 + - - +
646B GLU* 3.4 10.9 - - + +
651B GLN* 4.5 10.3 - - + -
654B VAL* 3.4 23.6 - - - -
655B ASP* 3.7 14.1 - - - +
658B ARG* 3.6 43.7 - - - +
705B HIS* 5.6 0.2 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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