Contacts of the helix formed by residues 630 - 639 (chain A) in PDB entry 5XJY
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 ASP 630 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ARG* 5.7 5.1 + - - -
46A TYR 5.5 0.5 - - - +
47A PRO 4.9 0.3 - - - -
48A PRO* 3.2 29.3 - - - +
628A VAL* 4.2 7.5 - - + +
629A ASP* 1.3 79.7 + - - +
631A ILE* 1.3 56.0 + - - +
632A PHE* 3.1 4.0 - - - -
633A LEU* 2.8 39.4 + - + +
634A ARG* 2.9 18.1 + - + +
799A GLU* 6.0 2.7 - - + +
1472A LYS* 3.3 34.6 - - - +
1474A LEU* 4.8 8.0 - - + +
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Residues in contact with ILE 631 (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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46A TYR* 6.2 5.2 - - + -
573A TYR* 6.0 4.3 - - + +
575A ASP* 4.6 16.4 - - + +
629A ASP* 3.7 21.0 - - + +
630A ASP* 1.3 75.0 - - - +
632A PHE* 1.3 60.7 + - + +
634A ARG* 3.8 22.3 + - - +
635A VAL* 2.9 35.3 + - + +
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Residues in contact with PHE 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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39A LEU* 3.6 37.5 - - + -
42A VAL* 3.6 26.9 - - + +
43A ARG* 3.3 52.0 - - + +
46A TYR* 5.0 21.1 - + + +
630A ASP 3.1 1.2 - - - -
631A ILE* 1.3 81.0 - - + +
633A LEU* 1.3 53.9 + - - +
635A VAL* 4.5 8.3 - - + -
636A MET* 2.6 67.1 + - + +
709A LEU* 4.4 0.9 - - + -
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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
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43A ARG* 3.3 21.2 - - - +
630A ASP* 2.8 30.2 + - + +
632A PHE* 1.3 73.8 - - - +
634A ARG* 1.3 61.2 + - + +
636A MET* 4.3 4.0 - - + -
637A SER* 3.0 33.5 + - - -
709A LEU 3.4 25.8 - - - +
710A LEU* 3.7 17.7 - - + -
711A PRO* 6.0 0.7 - - + -
795A ALA* 5.4 1.1 - - + +
798A GLU* 3.7 21.8 - - + +
799A GLU* 3.4 33.0 - - + +
1472A LYS* 5.6 8.5 - - - +
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Residues in contact with ARG 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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573A TYR* 5.1 9.9 - - - -
574A TRP* 3.5 24.8 + - - -
575A ASP* 3.8 23.3 - - - +
576A PRO* 4.3 10.5 - - - +
629A ASP* 5.4 0.4 - - - -
630A ASP* 2.9 23.8 + - + +
631A ILE* 3.8 18.0 - - - +
632A PHE 3.2 0.2 - - - -
633A LEU* 1.3 78.7 - - + +
635A VAL* 1.3 63.8 + - - +
637A SER* 4.1 0.2 - - - -
638A ARG* 2.9 79.4 + - - +
795A ALA* 6.1 1.1 - - - -
799A GLU* 4.3 15.9 - - - +
1474A LEU* 4.5 24.8 - - + +
1524A LYS* 5.5 0.4 - - - +
1526A TRP* 5.5 4.0 - - - +
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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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631A ILE* 2.9 24.8 + - + +
632A PHE* 4.3 10.1 - - + +
634A ARG* 1.3 77.2 - - - +
636A MET* 1.3 55.6 + - - +
638A ARG* 4.2 7.2 - - + +
639A SER* 2.6 45.0 + - - +
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Residues in contact with MET 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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39A LEU* 4.5 6.1 - - + -
632A PHE* 2.6 51.5 + - + +
633A LEU* 4.2 10.5 - - + +
635A VAL* 1.3 80.7 - - - +
637A SER* 1.3 69.7 + - - +
639A SER* 3.0 8.6 + - - +
640A MET* 2.9 30.3 + - + -
643A PHE* 3.6 24.1 - - + -
709A LEU* 3.6 48.2 - - + -
710A LEU* 4.1 20.0 - - + -
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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
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633A LEU* 3.0 21.6 + - - -
636A MET* 1.3 84.2 - - - +
638A ARG* 1.3 65.5 + - - +
640A MET* 3.7 11.3 + - - +
710A LEU* 4.4 15.8 - - - +
791A CYS* 3.7 33.1 + - - +
794A PHE* 4.4 2.9 - - - +
795A ALA* 3.3 30.3 + - - +
798A GLU* 5.2 0.4 + - - -
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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
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634A ARG* 2.9 78.7 + - - +
635A VAL* 4.0 8.5 - - + +
637A SER* 1.3 77.2 - - - +
639A SER* 1.3 58.4 + - - +
640A MET 3.5 1.0 + - - -
641A PRO* 4.6 0.7 - - - +
761A TYR* 3.2 15.6 + - - -
765A VAL* 5.7 2.4 - - - +
792A GLU* 2.9 40.2 + - - +
795A ALA* 3.6 23.5 - - - +
796A LEU* 4.4 12.7 - - - +
799A GLU* 6.0 1.1 - - - -
1521A LEU* 5.4 2.2 - - - +
1524A LYS* 3.4 27.2 - - - +
1526A TRP* 5.4 0.6 - - - -
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Residues in contact with SER 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 VAL* 2.6 31.5 + - - +
636A MET* 3.0 6.2 + - - -
638A ARG* 1.3 76.5 - - - +
640A MET* 1.3 64.3 + - - +
641A PRO* 3.5 5.8 - - - -
642A LEU* 3.9 21.9 + - - +
643A PHE* 3.2 15.9 - - - -
758A TYR* 5.6 1.8 - - - -
761A TYR* 5.2 3.1 - - - -
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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