Contacts of the helix formed by residues 629 - 646 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ALA* 3.6 24.4 - - + +
627A HIS* 2.8 33.5 + - - +
628A VAL* 1.3 87.6 + - + +
630A SER* 1.3 64.6 + - - +
631A ASP* 3.3 5.2 - - + +
632A VAL* 3.4 12.8 + - + +
633A LEU* 3.3 22.2 + - - +
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Residues in contact with SER 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A VAL 3.5 3.2 + - - -
629A GLU* 1.3 72.9 - - - +
631A ASP* 1.3 65.5 + - - +
633A LEU* 4.1 6.9 - - - +
634A GLU* 3.0 34.6 + - - +
700A SER* 4.8 4.9 + - - -
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Residues in contact with ASP 631 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ALA 6.5 0.2 - - - -
590A ALA* 4.2 15.8 - - + +
629A GLU* 3.3 3.5 - - + +
630A SER* 1.3 84.9 + - - +
632A VAL* 1.3 59.2 + - + +
634A GLU* 3.9 9.3 - - - +
635A ALA* 3.0 29.3 + - - +
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Residues in contact with VAL 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A ALA* 3.4 45.3 - - + +
589A VAL* 4.6 5.2 - - + -
590A ALA* 4.6 5.8 - - + +
593A LEU* 4.6 0.8 - - + +
623A VAL* 3.4 33.7 - - + +
627A HIS* 3.7 18.8 - - + +
629A GLU* 3.4 18.4 + - + +
630A SER 3.3 0.4 - - - -
631A ASP* 1.3 73.4 - - + +
633A LEU* 1.3 59.3 + - + +
635A ALA* 2.9 9.1 + - - +
636A CYS* 2.8 35.0 + - - -
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624A VAL* 4.1 20.9 - - + +
627A HIS 3.4 20.6 - - - +
628A VAL* 3.9 18.8 - - - +
629A GLU 3.3 18.5 + - - +
630A SER* 4.1 2.5 - - - +
632A VAL* 1.3 82.7 - - + +
634A GLU* 1.3 56.5 + - - +
636A CYS* 3.2 6.5 + - - +
637A SER* 2.8 30.3 + - - -
696A LYS* 3.9 20.2 - - + +
697A ARG* 3.8 25.4 - - + +
700A SER* 3.3 28.9 - - - +
701A PHE* 4.0 4.8 - - + -
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Residues in contact with GLU 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A SER* 3.0 23.2 + - - +
631A ASP* 3.9 10.5 - - - +
633A LEU* 1.3 76.6 - - - +
635A ALA* 1.3 57.2 + - - +
637A SER* 3.3 7.8 + - - -
638A LYS* 2.9 58.1 + - + +
700A SER* 4.4 7.7 - - - +
703A ASN* 6.3 1.1 - - - +
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Residues in contact with ALA 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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590A ALA* 4.2 10.5 - - + +
593A LEU* 3.8 25.9 - - + +
594A GLN* 4.2 17.7 - - - +
631A ASP 3.0 14.6 + - - +
632A VAL 2.9 9.9 + - - +
634A GLU* 1.3 77.0 - - - +
636A CYS* 1.3 58.1 + - - +
638A LYS* 3.5 6.3 + - - +
639A THR* 3.0 34.1 + - - -
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Residues in contact with CYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU* 3.8 13.2 - - - +
620A ILE* 4.1 15.8 - - + +
623A VAL* 3.6 26.9 - - - -
624A VAL* 3.5 34.5 - - + -
632A VAL* 2.8 22.3 + - - -
633A LEU* 3.4 9.2 - - - +
635A ALA* 1.3 69.6 - - - +
637A SER* 1.3 64.9 + - - +
639A THR* 3.1 13.0 + - - -
640A TYR* 3.1 21.2 + - - -
701A PHE* 4.2 3.1 - - + -
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Residues in contact with SER 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A LEU 2.8 19.4 + - - -
634A GLU* 3.5 8.5 - - - -
636A CYS* 1.3 74.2 - - - +
638A LYS* 1.3 63.9 + - - +
640A TYR 3.4 0.5 + - - -
641A SER* 3.2 10.2 + - - -
700A SER 3.8 8.4 + - - -
701A PHE* 3.6 31.4 + - - -
704A ALA* 4.0 9.1 - - - +
705A HIS* 2.9 44.3 + - - -
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Residues in contact with LYS 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593A LEU 6.1 0.4 - - - +
594A GLN* 6.1 1.3 - - - +
634A GLU* 2.9 48.3 + - + +
635A ALA* 3.7 7.2 - - - +
637A SER* 1.3 74.9 - - - +
639A THR* 1.3 62.9 + - - +
641A SER* 3.3 9.1 - - - -
642A ILE* 3.1 35.0 + - + +
704A ALA* 5.7 1.3 - - - -
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Residues in contact with THR 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A LEU* 3.4 30.9 + - + +
596A PRO* 4.1 24.3 - - + +
616A LEU* 4.6 0.7 - - + -
620A ILE* 3.4 30.1 - - + -
635A ALA 3.0 18.6 + - - -
636A CYS* 3.1 4.9 + - - -
638A LYS* 1.3 72.6 - - - +
640A TYR* 1.3 67.2 + - - +
642A ILE* 3.2 9.8 + - - +
643A LEU* 3.0 32.0 + - + +
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Residues in contact with TYR 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A LEU* 4.1 24.7 + - + -
620A ILE* 3.5 33.4 - - + +
621A LYS* 4.0 12.1 + - - +
636A CYS 3.1 24.4 + - - -
637A SER 3.7 5.4 - - - +
639A THR* 1.3 76.1 - - - +
641A SER* 1.3 62.9 + - - +
643A LEU* 3.2 6.1 + - - +
644A CYS* 3.0 28.7 + - - -
654A VAL* 3.9 18.1 - - + +
657A ALA* 4.8 4.4 + - + +
658A ARG* 4.0 30.1 - - + +
661A LEU* 3.2 36.4 - - + +
701A PHE* 3.4 20.4 - + - -
705A HIS* 3.7 14.8 - - + -
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Residues in contact with SER 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A SER 3.2 8.8 + - - -
638A LYS* 3.3 15.0 - - - -
639A THR 3.2 0.4 - - - -
640A TYR* 1.3 79.7 - - - +
642A ILE* 1.3 63.9 + - - +
644A CYS* 3.8 2.8 - - - +
645A SER* 3.1 29.8 + - - -
646A GLU* 4.4 1.4 - - - +
704A ALA* 3.8 25.6 + - - +
705A HIS* 3.6 11.3 - - - -
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Residues in contact with ILE 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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593A LEU 5.8 2.5 - - - +
596A PRO* 4.0 25.6 - - + +
597A GLN* 3.7 34.3 - - + +
601A LEU* 3.2 33.3 - - + +
638A LYS* 3.1 27.6 + - + +
639A THR* 3.7 9.2 - - - +
641A SER* 1.3 75.8 - - - +
643A LEU* 1.3 66.7 + - + +
646A GLU* 3.5 28.2 - - - +
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Residues in contact with LEU 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596A PRO* 5.2 4.7 - - + -
601A LEU* 3.7 25.1 - - + +
604A TYR* 4.0 16.6 - - + -
613A LEU* 4.2 10.8 - - + -
616A LEU* 3.9 26.7 - - + -
617A LEU* 4.0 23.3 - - + -
620A ILE* 4.4 2.9 - - + -
639A THR* 3.0 32.3 + - + +
640A TYR* 3.7 5.4 - - - +
642A ILE* 1.3 80.8 - - + +
644A CYS* 1.3 64.8 + - - +
646A GLU 4.5 0.7 + - - -
647A GLU 4.8 1.0 + - - -
650A ILE* 3.1 27.6 - - + +
654A VAL* 3.7 17.3 - - + -
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Residues in contact with CYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640A TYR 3.0 20.8 + - - +
641A SER* 3.8 4.7 - - - +
642A ILE 3.3 0.2 - - - -
643A LEU* 1.3 78.8 - - - +
645A SER* 1.3 60.8 + - - +
646A GLU 2.7 17.5 + - - -
647A GLU 3.5 15.2 + - - +
651A GLN* 3.7 17.6 - - + +
654A VAL* 3.6 22.4 - - - -
655A ASP* 3.0 29.8 - - - +
658A ARG* 3.8 16.4 - - - -
705A HIS* 5.8 0.7 - - - -
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Residues in contact with SER 645 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A SER* 3.1 17.9 + - - -
644A CYS* 1.3 78.8 - - - +
646A GLU* 1.3 67.0 + - - +
647A GLU 3.6 2.6 + - - -
651A GLN* 4.7 10.4 - - - +
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Residues in contact with GLU 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A LEU* 3.7 19.6 - - + +
641A SER 4.7 0.5 - - - +
642A ILE* 3.5 37.3 - - - +
644A CYS 2.7 4.4 + - - -
645A SER* 1.3 92.4 + - - +
647A GLU* 1.3 66.4 + - - +
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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
------------------------------------------------------------
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