Contacts of the strand formed by residues 632 - 638 (chain A) in PDB entry 5MJA
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 632 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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624A VAL* 4.4 17.0 - - + +
626A GLY 3.7 11.7 - - - +
627A ALA* 4.5 3.8 - - + +
631A GLY* 1.3 76.6 - - - -
633A VAL* 1.3 62.4 + - - +
634A TYR* 3.5 33.2 + - + +
650A ILE 3.6 1.2 - - - +
651A LYS* 3.8 1.6 - - - +
652A THR* 3.0 35.2 + - - -
654A LYS* 3.8 30.4 + - - +
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Residues in contact with VAL 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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624A VAL* 3.5 5.0 - - - +
625A ILE* 2.8 38.6 + - + -
626A GLY* 2.9 23.3 + - - +
627A ALA 4.2 20.6 - - - +
628A GLY* 4.4 1.3 - - - +
632A GLU* 1.3 74.9 - - - +
634A TYR* 1.3 60.2 + - - +
649A ALA* 4.3 0.2 - - + -
650A ILE 3.3 4.7 - - - +
651A LYS* 3.8 27.1 - - + -
901A 7O3 3.7 50.7 - - + +
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Residues in contact with TYR 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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621A ILE* 3.6 23.6 - - + -
622A GLU 3.5 18.6 - - - -
623A GLU 3.3 5.4 - - - +
624A VAL* 3.4 26.5 - - + +
625A ILE* 3.6 6.3 - - - +
632A GLU* 3.5 31.3 + - + -
633A VAL* 1.3 76.5 - - - +
635A LYS* 1.3 68.7 + - - +
649A ALA* 3.3 4.9 - - - -
650A ILE* 2.7 49.5 + - + +
652A THR* 3.2 34.9 + - + -
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Residues in contact with LYS 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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621A ILE* 4.2 0.5 - - - -
622A GLU* 2.8 31.7 + - - +
623A GLU* 2.8 37.5 + - - +
625A ILE* 3.7 21.5 - - + +
634A TYR* 1.3 78.6 - - - +
636A GLY* 1.3 62.9 + - - +
647A PTR 3.5 49.1 + - + -
648A VAL 3.5 7.4 - - - +
650A ILE* 4.5 0.7 - - - -
699A PHE* 3.7 41.2 - - + -
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Residues in contact with GLY 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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620A LYS 3.1 13.9 - - - -
622A GLU* 4.1 6.5 - - - -
635A LYS* 1.3 76.3 - - - +
637A ARG* 1.3 63.6 + - - -
647A PTR 3.4 14.0 - - - -
648A VAL* 2.8 32.7 + - - -
650A ILE* 3.7 11.6 - - - +
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Residues in contact with ARG 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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618A PHE 3.6 1.0 - - - +
619A VAL* 3.5 6.4 - - - +
620A LYS* 2.9 44.2 + - + +
622A GLU* 2.8 32.6 + - - +
636A GLY* 1.3 79.3 - - - +
638A LEU* 1.3 61.4 + - - +
639A LYS 4.2 0.2 - - - -
645A GLU* 3.2 40.2 + - + +
646A ILE 3.3 4.7 - - - +
647A PTR 3.0 52.3 + - + -
648A VAL* 3.8 2.2 - - - +
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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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614A ILE* 4.0 17.5 - - + -
618A PHE* 3.5 22.9 - - + +
619A VAL* 4.2 7.0 - - + -
637A ARG* 1.3 75.7 - - - +
639A LYS* 1.4 60.5 + - - +
640A LEU* 4.0 37.3 + - + +
644A ARG 4.3 0.9 - - - +
645A GLU* 3.3 3.8 - - - -
646A ILE* 2.9 45.7 + - + +
648A VAL* 3.7 23.7 - - + +
684A GLU* 3.8 35.2 - - + +
696A ILE* 4.6 4.0 - - + -
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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