Contacts of the strand formed by residues 648 - 659 (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 LEU 648 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A ARG* 2.8 23.7 + - - -
611A ASP* 3.6 27.2 + - - +
614A ARG* 3.6 30.7 - - + +
615A LEU* 4.1 22.4 - - + +
618A TYR* 5.4 0.2 - - + -
646A LYS 3.8 3.4 + - - -
647A LYS* 1.3 71.2 - - - +
649A VAL* 1.3 55.1 + - - +
650A HIS 3.3 28.9 - - - +
651A GLU* 4.1 15.5 - - + +
669A LEU* 4.0 16.2 - - + -
670A LEU 3.8 0.9 - - - +
671A LEU* 3.6 21.8 - - + -
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Residues in contact with VAL 649 (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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607A ARG* 3.8 14.1 + - - +
647A LYS* 3.3 5.8 + - + +
648A LEU* 1.3 73.6 - - - +
650A HIS* 1.3 66.7 + - + +
670A LEU* 2.8 40.1 + - + +
671A LEU 4.3 8.3 - - - -
672A ASP* 4.3 4.9 - - - +
754A LEU* 4.7 11.7 - - + +
758A THR* 3.9 28.3 - - + +
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Residues in contact with HIS 650 (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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648A LEU* 3.3 10.8 - - - +
649A VAL* 1.3 86.3 - - + +
651A GLU* 1.3 76.6 + - - +
670A LEU* 2.7 41.4 + - + -
750A ASN* 3.8 26.3 + - - -
751A TRP* 3.7 32.6 - + - -
754A LEU* 3.3 28.8 - - + +
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Residues in contact with GLU 651 (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 ARG* 3.4 30.7 + - - -
618A TYR* 2.7 37.1 + - - -
648A LEU* 4.1 10.7 - - + +
650A HIS* 1.3 91.9 + - - +
652A GLY* 1.3 58.2 + - - +
667A HIS* 3.0 15.4 + - - +
668A VAL 2.9 15.7 - - - +
669A LEU* 3.6 9.9 - - + -
751A TRP* 3.7 6.7 - - - -
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Residues in contact with GLY 652 (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* 1.3 77.0 - - - +
653A PRO* 1.3 77.9 - - - +
654A LEU* 3.7 5.7 + - - +
667A HIS* 3.8 11.9 + - - -
668A VAL* 2.9 28.9 + - - +
751A TRP* 3.6 11.1 - - - -
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Residues in contact with PRO 653 (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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652A GLY* 1.3 82.8 - - - +
654A LEU* 1.3 79.2 - - - +
665A GLU* 5.9 1.3 - - - +
666A VAL 3.5 9.4 - - - +
667A HIS* 3.8 15.7 - - + +
742A ALA* 5.4 0.2 - - - -
743A GLN* 4.2 26.0 - - - +
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Residues in contact with LEU 654 (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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652A GLY 3.7 1.8 - - - +
653A PRO* 1.3 101.0 - - - +
655A THR* 1.3 65.7 + - - +
665A GLU* 2.9 18.1 - - - +
666A VAL* 3.0 29.9 + - + +
668A VAL* 4.5 8.7 - - + -
725A PHE* 4.0 30.1 - - + -
740A LEU* 4.1 16.4 - - + -
741A VAL 3.6 15.3 - - - +
742A ALA* 4.2 6.3 - - + +
743A GLN* 4.3 6.2 + - - +
751A TRP* 3.2 50.0 - - + +
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Residues in contact with THR 655 (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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654A LEU* 1.3 73.6 - - - +
656A TRP* 1.3 64.7 + - - +
657A ARG* 3.8 2.5 - - + +
663A ALA* 3.8 25.6 - - + -
664A VAL 3.8 4.3 - - - +
665A GLU* 2.8 30.5 + - - +
740A LEU* 3.2 6.4 - - - +
741A VAL* 2.7 60.5 + - + +
743A GLN* 5.3 3.3 + - - -
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Residues in contact with TRP 656 (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* 1.3 73.5 - - - +
657A ARG* 1.3 68.5 + - - +
658A VAL* 2.8 18.5 + - + -
663A ALA* 4.5 0.2 - - - -
664A VAL* 3.1 58.3 + - + +
666A VAL* 3.7 21.1 - - + -
677A LEU* 3.9 16.5 - - + +
679A GLN* 5.9 0.2 - - + -
688A LYS 5.9 0.2 + - - -
690A HIS* 3.7 18.7 + + - -
704A LEU* 2.9 40.6 - - + -
705A ARG 4.6 3.3 + - - -
706A PRO* 5.9 2.4 - - - +
737A ILE 4.4 0.2 - - - -
738A TYR* 3.1 49.4 - + + -
739A GLU 3.6 12.3 - - - -
740A LEU* 3.4 20.6 - - + -
483B GLN* 5.7 0.2 - - - -
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Residues in contact with ARG 657 (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 1.5 - - + +
656A TRP* 1.3 71.9 - - - +
658A VAL* 1.3 65.1 + - - +
659A THR* 3.3 13.3 + - - +
660A LYS* 5.4 13.9 - - - +
662A LYS 3.9 4.9 - - - -
663A ALA* 4.4 16.4 - - + +
718A VAL* 6.1 0.2 - - - +
720A THR* 5.9 0.4 + - - -
721A ASP* 2.9 33.2 + - - +
739A GLU* 2.9 52.0 + - - +
741A VAL* 3.9 25.1 - - + +
483B GLN* 3.5 18.0 + - - -
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Residues in contact with VAL 658 (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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656A TRP* 2.8 24.4 + - + +
657A ARG* 1.3 71.9 - - - +
659A THR* 1.3 70.5 + - + +
662A LYS* 3.2 49.8 + - + +
664A VAL* 3.9 11.9 - - + -
690A HIS 3.6 23.1 - - - +
691A SER* 4.0 17.0 - - - -
704A LEU* 4.1 20.5 - - + +
483B GLN* 4.2 8.8 + - - +
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Residues in contact with THR 659 (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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657A ARG* 3.9 15.1 - - - +
658A VAL* 1.3 85.3 - - + +
660A LYS* 1.3 59.0 + - - +
661A ASP* 2.8 18.4 + - - +
662A LYS* 2.8 40.0 + - - +
691A SER 6.4 2.0 - - - -
739A GLU* 5.8 0.7 - - - -
483B GLN* 5.2 10.8 - - - +
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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