Contacts of the helix formed by residues 631 - 646 (chain A) in PDB entry 5G04
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 LYS 631 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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630A PRO* 1.3 76.8 - - - +
632A GLU* 1.3 66.6 + - - +
633A ILE 3.4 1.6 - - - -
634A ALA* 3.7 7.9 + - - +
635A VAL* 3.3 26.3 + - - +
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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
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630A PRO* 4.2 8.9 - - + +
631A LYS* 1.3 79.1 - - - +
633A ILE* 1.3 64.9 + - + +
635A VAL* 3.1 22.6 - - - +
636A GLN* 3.3 14.8 - - - +
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Residues in contact with ILE 633 (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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629A LEU* 3.8 19.3 - - + -
630A PRO* 3.7 21.8 - - + +
631A LYS 3.4 0.2 - - - -
632A GLU* 1.3 75.1 - - + +
634A ALA* 1.3 57.3 + - - +
635A VAL 3.1 2.2 - - - -
636A GLN* 2.7 33.8 + - + +
637A MET* 2.9 16.5 + - + +
756A PHE* 3.7 28.3 - - + -
758A HIS* 3.5 38.6 - - + +
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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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626A LYS* 4.7 20.6 - - + -
629A LEU* 3.4 23.3 - - + +
630A PRO 4.3 7.2 - - - +
631A LYS* 3.8 10.1 - - - +
633A ILE* 1.3 74.9 - - - +
635A VAL* 1.3 63.1 + - - +
637A MET* 4.3 9.6 - - + -
638A LEU* 3.1 32.3 + - + +
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Residues in contact with VAL 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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504A VAL* 3.6 47.6 - - + +
631A LYS 3.3 16.3 + - - +
632A GLU* 3.1 15.0 - - - +
634A ALA* 1.3 79.6 - - - +
636A GLN* 1.3 76.6 + - + +
638A LEU* 4.9 0.3 - - - +
639A VAL* 3.0 29.5 + - + +
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Residues in contact with GLN 636 (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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632A GLU* 3.3 22.4 + - - +
633A ILE* 2.7 20.5 + - + +
635A VAL* 1.3 89.2 - - + +
637A MET* 1.3 58.0 + - - +
639A VAL* 3.4 12.5 - - + +
640A LYS* 3.2 24.4 - - - +
667A MET* 5.4 0.4 - - - +
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Residues in contact with MET 637 (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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622A LEU* 4.7 15.7 - - + -
625A ILE* 3.5 34.8 - - + -
626A LYS* 5.9 1.8 - - - +
629A LEU* 5.1 5.4 - - + -
633A ILE* 2.9 19.0 + - + +
634A ALA* 4.0 13.0 - - + +
636A GLN* 1.3 76.4 - - - +
638A LEU* 1.3 76.7 + - + +
640A LYS* 3.3 5.2 + - - +
641A TRP* 3.2 19.3 + - - +
664A LEU* 4.0 17.9 - - + -
667A MET* 3.6 49.4 - - + +
762A ILE* 5.8 0.9 - - + -
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Residues in contact with LEU 638 (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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436A LEU* 3.8 44.6 - - + -
501A THR* 5.8 0.7 - - + -
612A ILE* 3.8 23.6 - - + -
622A LEU* 5.3 10.1 - - + +
626A LYS* 4.8 18.8 - - + -
634A ALA* 3.1 19.8 + - + +
635A VAL 4.9 0.4 - - - +
637A MET* 1.3 84.6 - - + +
639A VAL* 1.3 56.7 + - - +
641A TRP* 3.1 11.8 + - + +
642A TYR* 2.6 45.5 + - + +
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Residues in contact with VAL 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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504A VAL* 6.1 4.5 - - + -
505A ARG 3.5 25.4 - - - +
506A VAL* 3.5 28.6 - - + +
635A VAL* 3.0 27.4 + - + +
636A GLN* 3.4 13.0 - - + +
638A LEU* 1.3 74.7 - - - +
640A LYS* 1.3 71.9 + - + +
642A TYR* 3.9 6.0 - - - +
643A ASN* 3.1 27.2 + - - +
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Residues in contact with LYS 640 (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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636A GLN 3.2 17.7 - - - +
637A MET* 3.3 7.4 + - - +
638A LEU 3.1 0.6 - - - -
639A VAL* 1.3 86.8 + - + +
641A TRP* 1.3 63.1 + - - +
643A ASN* 3.7 11.6 + - - +
644A VAL* 3.3 26.0 + - + +
663A CYS 5.7 0.7 - - - +
666A ASN* 6.3 3.6 - - + -
667A MET* 4.6 15.3 - - + -
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Residues in contact with TRP 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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612A ILE* 2.7 36.1 - - + -
613A ALA* 4.0 2.5 - - - -
618A VAL* 3.8 28.5 - - + -
622A LEU* 3.3 28.5 - - + -
637A MET* 3.2 10.8 + - - +
638A LEU* 3.1 14.6 + - + +
640A LYS* 1.3 78.8 - - - +
642A TYR* 1.3 60.5 + - - +
644A VAL* 3.0 12.0 + - + +
645A HIS* 2.7 64.3 + + + +
656A GLU* 4.8 6.7 - - + -
659A LEU* 4.5 4.0 - - - +
660A PHE* 3.8 21.0 - + + +
663A CYS* 2.9 45.9 - - + +
667A MET* 4.6 2.0 - - + -
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Residues in contact with TYR 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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12A ILE* 3.6 37.7 - - + -
436A LEU* 5.1 3.1 - - + -
485A ILE* 3.6 12.3 - - + +
487A THR* 5.7 0.9 - - + -
499A LEU* 4.3 9.0 - - + +
506A VAL* 3.7 13.9 - - + -
609A ILE* 3.5 15.9 - - - +
610A PRO* 2.4 39.1 + - + -
611A GLU 4.4 1.3 - - - -
612A ILE* 3.5 39.9 - - + -
638A LEU* 2.6 28.9 + - + +
639A VAL* 3.4 7.8 + - - +
641A TRP* 1.3 76.3 - + - +
643A ASN* 1.3 61.7 + - - +
645A HIS* 3.4 18.5 + + - +
646A SER* 3.4 12.8 + - - -
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Residues in contact with ASN 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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11A MET* 3.6 47.3 + - - +
12A ILE* 4.0 8.9 + - - +
506A VAL 3.7 20.4 + - - +
507A GLY* 4.9 0.8 - - - -
639A VAL* 3.1 17.4 + - - +
640A LYS* 3.8 16.0 - - - +
642A TYR* 1.3 78.7 - - - +
644A VAL* 1.3 57.2 + - + +
646A SER* 3.0 22.8 + - - -
647A ALA 4.1 1.2 + - - -
648A PRO* 4.4 4.7 - - - +
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Residues in contact with VAL 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 LYS* 3.3 28.7 - - + +
641A TRP* 3.0 15.6 + - + +
643A ASN* 1.3 74.8 - - + +
645A HIS* 1.3 60.4 + - - +
647A ALA* 2.9 28.1 + - - +
659A LEU* 4.2 23.3 - - + +
662A THR* 5.3 6.3 - - - +
663A CYS* 5.8 5.6 - - + -
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Residues in contact with HIS 645 (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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15A ARG* 4.7 5.1 + - - -
610A PRO* 4.1 16.8 - - + +
611A GLU 2.8 22.7 + - - -
612A ILE* 3.4 22.9 + - - -
613A ALA 4.1 4.4 + - - -
614A THR* 3.8 21.8 - - - -
641A TRP* 2.7 48.8 + + + +
642A TYR* 3.4 15.0 + + - +
644A VAL* 1.3 72.9 - - - +
646A SER* 1.3 65.3 + - - +
647A ALA* 3.3 6.2 + - - +
656A GLU* 5.9 4.1 - - + +
659A LEU* 5.5 5.4 - - - +
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Residues in contact with SER 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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12A ILE* 3.7 27.4 + - - +
13A ALA* 4.4 9.5 - - - +
610A PRO* 4.6 17.0 - - - -
642A TYR* 3.4 7.8 + - - -
643A ASN 3.0 20.9 + - - -
645A HIS* 1.3 82.8 - - - +
647A ALA* 1.3 66.0 + - - +
648A PRO* 3.3 15.6 - - - +
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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