Contacts of the helix formed by residues 630 - 644 (chain A) in PDB entry 4P3N
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 CYS 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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625A PRO* 4.2 4.7 - - + -
626A VAL* 5.1 1.1 - - - -
627A GLY 2.9 18.6 + - - +
629A THR* 1.3 81.7 - - - +
631A ASP* 1.3 56.8 + - - +
632A GLU 2.8 13.2 + - - -
633A TYR* 3.0 9.8 + - + +
634A ALA* 2.9 22.2 + - - +
676A VAL* 3.9 23.1 - - + +
677A GLY* 3.3 34.5 - - - +
678A GLU* 3.4 17.0 - - - -
681A LYS* 5.2 3.1 - - + -
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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
----------------------------------------------------------
625A PRO* 3.4 15.6 - - - +
627A GLY 3.6 0.9 + - - +
628A PRO* 2.9 41.6 + - - +
630A CYS* 1.3 76.2 - - - +
632A GLU* 1.3 60.0 + - - +
634A ALA* 4.0 2.2 - - - +
635A GLN* 3.5 26.8 + - - +
652A LEU* 3.3 40.8 - - + +
654A PRO* 5.7 3.3 - - - +
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Residues in contact with GLU 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A PRO 4.6 0.4 + - - -
629A THR 4.6 7.3 + - - +
630A CYS 2.8 1.9 + - - -
631A ASP* 1.3 77.9 - - - +
633A TYR* 1.3 67.1 + - - +
635A GLN* 2.9 18.1 + - - +
636A LYS* 3.1 10.9 + - + +
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Residues in contact with TYR 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630A CYS* 3.0 8.8 + - - +
632A GLU* 1.3 78.6 + - - +
634A ALA* 1.3 63.2 + - - +
636A LYS* 2.9 24.0 + - + +
637A VAL* 2.9 25.8 + - + +
676A VAL* 3.3 34.8 - - + -
680A GLU 3.2 21.8 - - - -
681A LYS* 3.4 35.2 - - + -
684A GLY* 3.0 7.8 - - - -
685A THR 2.5 43.5 + - - -
701A ILE* 3.7 15.8 - - + +
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Residues in contact with ALA 634 (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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623A VAL* 3.3 24.6 - - + +
625A PRO* 3.6 34.3 - - + -
630A CYS 2.9 11.8 + - - +
631A ASP 4.0 4.0 - - - +
633A TYR* 1.3 75.6 - - - +
635A GLN* 1.3 57.6 + - - +
637A VAL* 3.5 2.4 - - - +
638A ARG* 2.9 29.1 + - - +
650A ILE* 4.0 7.6 - - + -
676A VAL* 4.0 10.2 - - + +
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Residues in contact with GLN 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631A ASP* 3.5 14.5 + - - +
632A GLU* 2.9 10.9 + - - +
634A ALA* 1.3 77.1 - - - +
636A LYS* 1.3 61.0 + - - +
638A ARG* 3.8 7.1 - - + +
639A GLN* 3.0 28.5 + - - +
650A ILE* 3.9 20.7 - - + +
652A LEU* 3.7 28.2 - - - +
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Residues in contact with LYS 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A GLU 3.1 9.5 + - - +
633A TYR* 2.9 19.6 + - + +
635A GLN* 1.3 74.1 - - - +
637A VAL* 1.3 55.3 + - - +
639A GLN* 2.9 7.9 + - - +
640A GLN* 2.8 47.4 + - + +
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Residues in contact with VAL 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A VAL* 3.9 24.0 - - + -
633A TYR* 2.9 42.5 + - + +
634A ALA 3.5 7.6 - - - +
636A LYS* 1.3 75.2 - - - +
638A ARG* 1.3 65.1 + - - +
640A GLN* 2.9 20.2 + - - +
641A PHE* 3.0 31.1 + - + +
674A LEU* 4.2 10.5 - - + -
676A VAL* 4.3 3.8 - - + -
686A VAL* 4.0 18.6 - - + -
701A ILE* 4.1 11.4 - - + -
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Residues in contact with ARG 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A VAL* 3.8 13.2 - - + -
634A ALA 2.9 21.8 + - - +
635A GLN* 3.8 12.8 - - - +
637A VAL* 1.3 73.9 - - - +
639A GLN* 1.3 69.3 + - - +
641A PHE* 3.9 0.6 + - - -
642A HIS* 3.2 43.6 + - - +
648A ALA* 2.9 28.6 + - - +
649A ASP* 3.5 34.3 + - - +
650A ILE* 3.7 27.8 - - + +
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Residues in contact with GLN 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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635A GLN* 3.0 15.3 + - - +
636A LYS* 2.9 12.9 + - - +
638A ARG* 1.3 84.5 + - - +
640A GLN* 1.3 67.7 + - + +
642A HIS* 2.9 13.8 + - - +
643A ASP* 2.9 51.8 + - - +
365B ARG 5.8 0.2 + - - -
366B LYS* 4.8 11.5 + - - +
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Residues in contact with GLN 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636A LYS* 2.8 29.8 + - + +
637A VAL 2.9 5.7 + - - +
639A GLN* 1.3 73.0 - - + +
641A PHE* 1.3 59.0 + - - +
643A ASP* 2.9 13.8 + - - +
644A ALA* 2.8 27.0 + - - +
701A ILE* 3.2 41.3 - - + +
705A ILE* 4.4 16.8 - - + +
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Residues in contact with PHE 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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621A VAL* 4.0 15.7 - - + -
637A VAL* 3.0 24.1 + - + +
638A ARG* 4.6 0.7 - - - -
640A GLN* 1.3 77.4 - - - +
642A HIS* 1.3 61.8 + - - +
644A ALA* 3.3 11.4 + - - +
646A PHE* 3.1 46.7 + + + +
648A ALA* 4.0 17.7 - - + -
674A LEU* 3.5 24.5 - - + -
686A VAL* 5.5 2.0 - - + -
701A ILE* 4.2 13.9 - - + -
704A THR* 3.5 29.2 - - + -
705A ILE* 3.7 28.0 - - + -
708A LEU* 3.4 25.1 - - + -
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Residues in contact with HIS 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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638A ARG* 3.2 37.5 + - - +
639A GLN* 2.9 17.9 + - - +
641A PHE* 1.3 78.6 - - - +
643A ASP* 1.3 64.4 + - - +
645A LYS* 3.2 13.9 + - - -
646A PHE 3.7 18.9 + - - +
647A MET* 4.7 8.9 - - - -
648A ALA* 4.0 16.4 - - - +
365B ARG* 3.3 42.0 + - + +
368B GLY* 5.8 5.6 - - - -
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Residues in contact with ASP 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A GLN* 2.9 42.5 + - - +
640A GLN* 2.9 11.2 + - - +
642A HIS* 1.3 73.7 + - - +
644A ALA* 1.3 58.0 + - - +
645A LYS* 2.9 13.4 + - - +
365B ARG 5.0 2.0 - - - +
366B LYS* 4.6 24.8 - - + +
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Residues in contact with ALA 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 GLN 2.8 12.9 + - - +
641A PHE* 3.4 13.2 - - - +
642A HIS 3.2 0.4 - - - -
643A ASP* 1.3 73.6 - - - +
645A LYS* 1.3 59.7 + - - +
646A PHE* 3.3 24.9 + - + -
705A ILE* 3.7 21.5 - - + -
709A GLN* 2.9 32.8 + - - +
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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