Contacts of the strand formed by residues 670 - 680 (chain A) in PDB entry 2ODP
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 ARG 670 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263A ARG* 5.9 0.4 - - - +
266A SER* 3.4 27.8 + - - +
268A GLU* 2.8 34.7 + - - +
442A ILE* 3.5 17.6 - - - +
443A CYS* 2.8 39.8 + - - -
444A GLY* 3.2 10.7 + - - -
445A VAL* 3.6 11.1 - - - +
561A CYS* 5.0 0.4 - - - -
567A GLU* 4.6 1.6 + - - +
571A ALA* 3.5 30.3 - - + +
573A ARG* 6.0 0.7 - - - +
666A GLU* 3.3 4.0 - - - -
667A ARG 2.8 33.6 + - - +
668A ARG 3.5 12.1 - - - +
669A PHE* 1.3 83.5 - - - +
671A PHE* 1.3 66.3 + - - +
672A PHE* 3.3 19.5 - - + -
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Residues in contact with PHE 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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444A GLY* 2.9 27.0 + - - +
446A GLY* 3.9 18.6 - - - -
447A ASN 5.1 0.4 - - - -
448A MET* 3.7 40.2 - - + -
457A ARG 4.3 10.3 - - - -
460A TRP* 3.5 36.1 - + + -
560A ILE* 4.0 6.3 - - + -
561A CYS* 3.2 26.2 + - - +
596A HIS* 5.8 1.1 - + - -
604A LYS* 4.2 16.2 - - - -
664A PHE* 3.8 23.6 - + + -
665A LEU 3.4 2.2 - - - +
666A GLU* 3.8 28.7 - - + -
670A ARG* 1.3 73.3 - - - +
672A PHE* 1.3 63.2 + - - +
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Residues in contact with PHE 672 (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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560A ILE* 4.0 0.2 - - - -
561A CYS* 3.3 30.1 - - + +
563A PRO* 5.3 3.1 - - + -
568A ALA* 4.0 12.6 - - + -
571A ALA* 3.6 24.7 - - + -
572A LEU* 3.5 41.3 - - + -
587A LEU* 4.1 28.5 - - + -
664A PHE* 3.1 6.6 - - - -
665A LEU* 3.0 37.8 + - + +
667A ARG* 3.4 23.3 - - + -
670A ARG* 3.3 28.5 - - + -
671A PHE* 1.3 73.8 - - - +
673A GLN* 1.3 62.8 + - - +
674A VAL* 3.5 2.4 + - + -
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Residues in contact with GLN 673 (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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475A ALA* 3.5 12.1 - - - +
477A ILE* 4.2 0.7 - - - +
483A LEU* 3.7 29.2 + - - +
560A ILE* 3.4 32.0 - - + +
561A CYS 2.9 9.1 + - - -
562A LEU* 3.8 18.2 - - + +
563A PRO* 2.9 24.5 - - - +
661A GLY 4.9 0.2 - - - -
662A ALA* 3.5 21.6 - - + +
663A VAL 3.6 6.3 - - - +
672A PHE* 1.3 71.8 - - - +
674A VAL* 1.3 59.4 + - - +
675A GLY 3.1 27.8 + - - +
676A LEU* 3.9 10.3 - - - +
712A LEU* 3.6 9.8 - - + +
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Residues in contact with VAL 674 (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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563A PRO* 4.9 0.2 - - - -
587A LEU* 4.2 15.7 - - + -
588A LEU* 4.4 6.7 - - + -
609A LEU* 3.9 17.3 - - + -
644A LEU* 3.8 11.7 - - + +
663A VAL* 2.9 15.8 + - + +
665A LEU* 3.5 47.6 - - + -
672A PHE 3.5 1.7 + - - +
673A GLN* 1.3 76.2 - - - +
675A GLY* 1.3 59.8 + - - +
711A ASN* 3.7 8.7 + - - -
712A LEU* 2.8 27.2 + - - +
713A PHE* 4.0 26.8 + - + -
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Residues in contact with GLY 675 (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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644A LEU* 4.1 8.7 - - - -
663A VAL* 2.8 30.4 + - - -
673A GLN* 3.1 16.7 + - - +
674A VAL* 1.3 81.8 - - - +
676A LEU* 1.3 61.6 + - - -
710A ILE 2.9 15.5 - - - -
712A LEU* 4.0 6.5 - - - -
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Residues in contact with LEU 676 (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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483A LEU* 4.1 10.8 - - + +
484A THR 3.6 17.5 - - - +
485A ALA* 3.8 17.9 - - + +
541A ASP 3.6 19.5 - - - +
542A ILE* 3.8 25.4 - - + -
660A GLY* 4.0 7.4 - - - +
661A GLY 3.2 12.6 - - - +
663A VAL* 4.1 1.9 - - - +
673A GLN* 3.9 7.4 - - - +
675A GLY* 1.3 75.4 - - - +
677A VAL* 1.3 80.1 + - - +
678A SER* 4.8 0.4 - - - +
709A HIS* 3.2 7.8 - - - +
710A ILE* 3.0 41.2 + - + -
712A LEU* 4.1 11.4 - - + -
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Residues in contact with VAL 677 (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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485A ALA* 4.0 2.4 - - - +
597A PHE* 4.2 14.8 - - + -
654A PRO* 3.4 42.2 - - + -
655A CYS 5.0 1.1 - - - +
658A GLU 3.7 15.5 - - - +
659A SER* 3.7 22.6 - - - +
660A GLY* 2.8 24.4 + - - +
661A GLY* 2.9 16.7 + - - +
663A VAL* 3.8 15.9 - - + -
676A LEU* 1.3 77.1 - - - +
678A SER* 1.3 64.2 + - - +
679A TRP* 5.0 2.2 - - - +
709A HIS* 4.0 8.3 - - + -
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Residues in contact with SER 678 (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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487A HIS* 3.1 22.7 + - - -
538A TYR* 3.6 7.4 - - - +
541A ASP* 2.7 30.5 + - - +
643A PHE* 3.7 4.1 - - - -
659A SER* 3.7 6.5 + - - -
676A LEU* 3.3 2.3 + - - -
677A VAL* 1.3 77.9 - - - +
679A TRP* 1.3 80.4 + - - +
708A PHE 3.3 15.3 + - - -
709A HIS* 4.6 0.2 - - - -
710A ILE* 4.0 20.4 - - - -
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Residues in contact with TRP 679 (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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538A TYR* 3.4 43.3 - + + +
622A VAL* 4.0 10.8 - - + -
629A PHE* 3.6 32.1 - + - -
638A VAL* 3.8 24.0 + - + -
639A VAL* 4.1 6.1 - - + -
643A PHE* 3.3 26.2 - + - -
677A VAL* 5.0 2.7 - - - +
678A SER* 1.3 98.0 - - - +
680A GLY* 1.3 77.4 + - - +
681A LEU* 4.0 11.2 - - + -
707A ASP* 3.5 4.6 - - - +
708A PHE* 2.7 69.6 + + + +
709A HIS* 5.3 0.7 - - - -
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Residues in contact with GLY 680 (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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679A TRP* 1.3 93.5 - - - +
681A LEU* 1.3 65.2 - - - +
682A TYR 3.5 3.6 - - - -
706A ARG 3.1 13.7 - - - -
707A ASP* 3.9 9.0 - - - -
708A PHE* 4.4 0.9 - - - -
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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