Contacts of the strand formed by residues 663 - 671 (chain B) in PDB entry 3ODO
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 ALA 663 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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655B THR* 3.8 21.5 - - + -
656B TRP 3.2 9.6 - - - +
657B ARG* 4.4 12.8 - - + +
661B ASP 4.2 0.8 + - - -
662B LYS* 1.3 77.4 - - - +
664B VAL* 1.3 68.1 - - - +
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Residues in contact with VAL 664 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655B THR* 3.5 3.4 - - - -
656B TRP* 2.9 39.1 + - + +
658B VAL* 4.6 9.6 - - + -
662B LYS* 4.6 15.0 - - + -
663B ALA* 1.3 82.2 - - - +
665B GLU* 1.3 75.9 + - - +
666B VAL* 3.4 14.3 + - + -
679B GLN* 3.8 27.4 - - - +
690B HIS* 4.2 22.4 - - + +
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Residues in contact with GLU 665 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654B LEU 3.9 5.8 - - - +
655B THR* 4.5 11.0 - - + +
664B VAL* 1.3 79.5 - - - +
666B VAL* 1.3 64.1 + - - +
679B GLN* 4.2 11.6 - - - +
680B ARG 4.9 1.2 + - - -
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Residues in contact with VAL 666 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653B PRO* 3.4 6.3 - - - +
654B LEU* 2.9 47.9 + - + +
656B TRP* 3.8 37.2 - - + +
664B VAL* 3.8 10.5 - - + +
665B GLU* 1.3 78.0 - - - +
667B HIS* 1.3 60.9 + - - +
668B VAL* 3.8 18.4 - - + -
677B LEU* 4.2 11.0 - - + +
678B LEU 3.3 23.8 - - - +
679B GLN* 4.3 2.9 - - + +
680B ARG 5.6 0.4 - - - +
740B LEU* 4.5 2.9 - - + -
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Residues in contact with HIS 667 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618B TYR* 4.1 10.3 + + - -
651B GLU* 3.7 28.3 + - + +
652B GLY* 3.8 26.2 - - - -
653B PRO* 3.9 11.5 - - + +
666B VAL* 1.3 74.1 - - - +
668B VAL* 1.3 61.0 + - - +
669B LEU* 3.8 19.5 - - + -
676B LEU 3.6 0.7 - - - +
678B LEU* 2.6 52.0 + - + +
680B ARG* 3.2 41.2 + - - +
685B LEU* 5.2 3.1 - - + -
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Residues in contact with VAL 668 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651B GLU* 3.0 26.5 - - - -
652B GLY 2.8 17.2 + - - +
654B LEU* 3.7 25.6 - - + -
666B VAL* 3.8 22.7 - - + +
667B HIS* 1.3 75.9 - - - +
669B LEU* 1.3 67.8 + - - +
675B LEU* 3.7 27.8 - - + -
676B LEU 3.4 8.3 - - - +
677B LEU* 4.0 15.0 - - + -
740B LEU* 4.6 1.8 - - + -
751B TRP* 3.7 19.8 - - + -
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Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B LEU* 4.7 0.4 - - + -
618B TYR* 4.2 13.5 - - + -
643B ILE* 4.0 19.7 - - + -
648B LEU* 4.3 6.1 - - + -
650B HIS 3.8 2.5 - - - -
651B GLU* 3.9 16.4 - - + +
667B HIS* 3.8 21.3 - - + -
668B VAL* 1.3 83.3 - - - +
670B LEU* 1.3 60.5 + - - +
671B LEU* 3.3 25.9 + - + +
674B LEU 3.5 0.3 - - - +
675B LEU* 3.3 2.9 - - - -
676B LEU* 2.9 54.0 + - + +
678B LEU* 3.5 25.4 - - + -
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Residues in contact with LEU 670 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649B VAL* 3.0 24.7 + - + +
650B HIS* 2.9 24.8 + - + +
668B VAL 3.9 1.4 + - - -
669B LEU* 1.3 71.2 - - - +
671B LEU* 1.3 80.3 + - - +
674B LEU 3.7 2.0 - - - +
675B LEU* 4.2 7.9 - - + -
710B LEU* 3.6 25.1 - - + -
751B TRP* 3.9 19.4 - - + -
754B LEU* 3.9 32.8 - - + +
755B ILE* 3.7 32.1 - - + -
758B THR* 3.8 14.6 - - + +
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Residues in contact with LEU 671 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615B LEU* 4.2 9.6 - - + -
643B ILE* 3.8 37.0 - - + +
646B LYS* 4.1 19.1 - - + -
647B LYS 3.3 13.7 - - - +
648B LEU* 3.9 15.5 - - + -
649B VAL* 3.5 5.3 - - - +
669B LEU* 3.3 25.9 + - + -
670B LEU* 1.3 93.8 - - - +
672B ASP* 1.3 69.4 + - - +
673B ASP* 3.2 3.4 + - - +
674B LEU* 2.7 27.0 + - + +
676B LEU* 4.5 15.0 - - + -
710B LEU* 3.7 0.3 - - - +
758B THR* 3.6 1.2 - - - +
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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