Contacts of the strand formed by residues 662 - 671 (chain A) in PDB entry 3ODX
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 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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658A VAL* 3.2 28.4 + - + +
659A THR* 2.8 39.4 + - - +
661A ASP* 1.3 82.2 - - + +
663A ALA* 1.3 64.8 + - - +
664A VAL* 4.2 11.4 - - - -
690A HIS* 3.7 32.3 + - - +
691A SER 5.3 3.6 - - - +
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Residues in contact with ALA 663 (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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655A THR* 3.8 23.1 - - + -
656A TRP 3.8 3.8 - - - -
657A ARG* 4.4 14.4 - - + -
661A ASP 4.3 0.8 - - - -
662A LYS* 1.3 79.3 - - - +
664A VAL* 1.3 63.1 + - - +
665A GLU* 4.2 2.6 + - - +
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Residues in contact with VAL 664 (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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655A THR* 3.8 2.8 - - - -
656A TRP* 3.1 55.8 + - + +
658A VAL* 3.9 14.6 - - + -
662A LYS* 4.2 9.0 - - - -
663A ALA* 1.3 77.6 - - - +
665A GLU* 1.3 69.4 + - - +
666A VAL* 3.6 1.9 + - + -
679A GLN* 3.3 38.1 - - + +
690A HIS* 3.2 30.3 - - + +
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Residues in contact with GLU 665 (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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653A PRO* 5.9 1.4 - - - +
654A LEU 2.9 23.1 + - - +
655A THR* 2.8 31.3 + - - +
663A ALA* 4.2 2.8 + - - +
664A VAL* 1.3 73.1 - - - +
666A VAL* 1.3 59.8 + - - +
679A GLN* 3.9 21.8 - - - +
680A ARG* 4.5 4.0 + - - +
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Residues in contact with VAL 666 (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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653A PRO* 3.5 4.5 - - - +
654A LEU* 3.0 46.6 + - + +
656A TRP* 3.7 30.7 - - + -
664A VAL* 4.0 6.5 - - + +
665A GLU* 1.3 76.6 + - - +
667A HIS* 1.3 58.2 + - - +
668A VAL* 4.1 17.9 - - + -
677A LEU* 3.5 18.8 - - + +
678A LEU 3.2 35.7 - - - +
679A GLN* 4.2 2.9 - - + +
680A ARG* 5.5 1.1 - - - +
740A LEU* 4.5 2.7 - - + -
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Residues in contact with HIS 667 (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 TYR* 4.2 7.8 + + - -
651A GLU* 3.0 33.4 + - - +
652A GLY* 3.7 25.5 - - - -
653A PRO* 3.8 10.9 - - + +
666A VAL* 1.3 72.3 - - - +
668A VAL* 1.3 63.3 + - - +
669A LEU* 4.0 13.9 - - + -
678A LEU* 2.6 49.4 + - + +
680A ARG* 3.3 38.7 + - + +
685A LEU* 5.3 6.1 - - + -
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Residues in contact with VAL 668 (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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651A GLU* 2.9 28.4 - - - +
652A GLY 2.9 16.3 + - - +
654A LEU* 4.5 14.6 - - + -
666A VAL* 4.1 14.4 - - + -
667A HIS* 1.3 74.6 - - - +
669A LEU* 1.3 72.7 + - - +
675A LEU* 4.3 18.6 - - + -
676A LEU 3.4 9.0 - - - +
677A LEU* 3.5 26.5 - - + -
740A LEU* 4.9 3.4 - - + -
751A TRP* 3.6 30.3 - - + -
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Residues in contact with LEU 669 (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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615A LEU* 4.9 1.8 - - + -
618A TYR* 3.5 41.1 - - + -
643A ILE* 4.4 17.7 - - + -
648A LEU* 4.0 7.2 - - + -
650A HIS 3.5 2.2 - - - -
651A GLU* 3.5 21.5 - - + +
667A HIS* 4.0 6.7 - - + -
668A VAL* 1.3 76.6 - - - +
670A LEU* 1.3 61.4 + - - +
671A LEU* 3.5 25.4 + - + +
675A LEU* 3.8 2.9 - - - +
676A LEU* 3.0 43.4 + - + +
678A LEU* 4.0 21.5 - - + -
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Residues in contact with LEU 670 (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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649A VAL* 2.8 50.8 + - + +
650A HIS* 2.7 26.4 + - + +
668A VAL* 4.1 1.2 + - - +
669A LEU* 1.3 70.1 - - - +
671A LEU* 1.3 65.2 + - - +
674A LEU 4.3 1.1 - - - +
675A LEU* 4.1 21.5 - - + -
710A LEU* 3.5 32.3 - - + -
751A TRP* 4.7 9.0 - - + -
754A LEU* 3.8 25.4 - - + -
755A ILE* 3.8 12.8 - - + +
758A THR* 3.7 15.5 - - - +
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Residues in contact with LEU 671 (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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615A LEU* 4.9 4.7 - - + -
643A ILE* 4.1 24.9 - - + +
646A LYS* 3.9 29.4 - - + -
647A LYS 3.2 14.4 - - - +
648A LEU* 3.6 14.1 - - + -
649A VAL* 4.3 4.0 - - - -
669A LEU* 3.5 31.0 - - + +
670A LEU* 1.3 85.8 - - - +
672A ASP* 1.3 76.1 + - - +
673A ASP 3.0 1.9 + - - -
674A LEU* 3.1 18.4 + - + +
676A LEU* 4.6 15.9 - - + -
710A LEU* 3.6 15.4 - - - +
758A THR* 3.9 2.3 - - - +
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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