Contacts of the strand formed by residues 648 - 656 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607B ARG* 2.8 28.5 + - - -
611B ASP* 3.8 28.2 + - - +
614B ARG* 3.7 31.9 - - + +
615B LEU* 4.2 24.4 - - + +
618B TYR* 5.4 0.2 - - + -
646B LYS 4.2 1.0 + - - -
647B LYS* 1.3 69.7 - - - +
649B VAL* 1.3 56.3 + - - +
650B HIS 3.4 27.6 - - - +
651B GLU* 4.5 11.4 - - + +
669B LEU* 3.8 16.8 - - + -
670B LEU 3.9 1.1 - - - +
671B LEU* 3.7 22.0 - - + -
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Residues in contact with VAL 649 (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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607B ARG* 3.8 15.7 + - - +
647B LYS* 3.5 3.7 + - + +
648B LEU* 1.3 74.2 - - - +
650B HIS* 1.3 68.7 + - + +
670B LEU* 2.9 37.9 + - + +
671B LEU 4.5 7.6 - - - -
672B ASP* 4.5 3.8 - - - +
754B LEU* 4.4 15.1 - - + +
758B THR* 3.9 32.3 - - + +
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Residues in contact with HIS 650 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B LEU* 3.4 9.7 - - - +
649B VAL* 1.3 92.9 - - + +
651B GLU* 1.3 80.4 + - - +
652B GLY* 5.6 0.2 - - - -
670B LEU* 2.9 35.2 + - + -
750B ASN* 3.6 17.7 + - - -
751B TRP* 3.7 33.9 - + - -
754B LEU* 3.3 34.0 - - + +
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Residues in contact with GLU 651 (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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614B ARG* 3.5 29.4 + - - -
618B TYR* 2.7 38.4 + - - -
648B LEU* 4.4 7.4 - - + -
650B HIS* 1.3 89.9 + - - +
652B GLY* 1.3 58.7 + - - +
667B HIS* 3.2 16.9 - - + +
668B VAL 3.1 14.6 - - - +
669B LEU* 3.4 8.3 - - + +
751B TRP* 3.9 7.4 - - - -
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Residues in contact with GLY 652 (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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650B HIS* 5.6 0.2 - - - -
651B GLU* 1.3 75.5 - - - +
653B PRO* 1.4 80.1 - - - +
667B HIS* 3.6 12.0 + - - -
668B VAL* 3.0 26.1 + - - +
751B TRP* 3.6 16.3 - - - -
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Residues in contact with PRO 653 (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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652B GLY* 1.4 88.0 - - - +
654B LEU* 1.3 72.3 + - - +
665B GLU* 5.2 4.9 - - - +
666B VAL 3.7 9.0 - - - +
667B HIS* 3.6 16.1 - - + +
742B ALA* 5.3 0.5 - - - -
743B GLN 5.7 0.5 + - - -
751B TRP* 4.3 2.8 + - - -
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Residues in contact with LEU 654 (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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652B GLY 4.2 0.9 - - - +
653B PRO* 1.3 84.1 - - - +
655B THR* 1.3 60.5 + - - +
656B TRP 4.1 0.4 - - - -
665B GLU* 2.7 24.8 - - - +
666B VAL* 3.0 18.8 + - + +
668B VAL* 3.8 25.8 - - + -
725B PHE* 4.0 21.8 - - + -
740B LEU* 4.0 19.3 - - + -
741B VAL 3.4 18.4 - - - +
742B ALA* 3.4 22.7 - - + +
743B GLN 5.9 0.4 - - - +
751B TRP* 3.6 34.8 - - + +
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Residues in contact with THR 655 (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* 1.3 74.8 - - - +
656B TRP* 1.3 59.9 + - - +
657B ARG* 3.4 14.8 + - + -
663B ALA* 4.1 26.0 - - + -
664B VAL 4.0 3.1 - - - +
665B GLU* 3.1 22.1 + - - +
740B LEU* 3.4 7.4 - - - -
741B VAL* 2.8 53.8 + - + +
743B GLN* 5.7 0.5 + - - -
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Residues in contact with TRP 656 (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 4.1 0.8 + - - -
655B THR* 1.3 70.2 - - - +
657B ARG* 1.3 61.2 + - - +
658B VAL* 3.1 15.7 + - + +
663B ALA* 3.7 0.3 - - - -
664B VAL* 2.8 69.2 + - + +
666B VAL* 3.8 16.8 - - + +
677B LEU* 3.7 19.3 - - + -
679B GLN* 5.1 1.1 - - - -
688B LYS* 3.5 42.4 - - + -
704B LEU* 3.9 38.5 - - + +
705B ARG 4.1 5.8 - - - -
706B PRO* 4.8 3.4 - - + -
738B TYR* 3.6 42.0 - + - +
739B GLU 3.7 7.4 - - - +
740B LEU* 3.6 24.2 - - + +
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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