Contacts of the strand formed by residues 701 - 708 (chain A) in PDB entry 2C11
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 VAL 701 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A ARG* 3.4 3.1 - - - -
489A PHE* 2.9 56.4 + - + +
608A LEU* 3.2 17.9 - - + +
609A SER* 4.3 2.0 - - - -
610A PHE* 3.9 25.1 - - + -
680A ALA* 3.9 12.3 - - + -
681A GLY* 4.0 9.0 - - - +
682A PHE* 3.9 31.0 - - + -
698A GLY 5.8 0.2 - - - +
699A ASN* 3.6 4.2 + - - +
700A GLY* 1.3 77.7 - - - +
702A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 702 (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 ILE* 2.9 13.2 - - - -
488A ARG* 4.7 0.4 - - - -
526A PHE* 5.2 5.4 - - - -
607A MET* 4.2 1.4 - - - +
608A LEU* 3.1 29.0 + - - +
678A VAL* 4.3 2.4 - - - +
680A ALA* 3.8 14.9 - - - +
701A VAL* 1.3 75.8 - - - +
703A PHE* 1.3 78.9 + - - +
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Residues in contact with PHE 703 (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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363A ILE* 4.7 1.6 - - + -
486A GLU* 3.5 3.8 - - - +
487A ILE* 2.9 67.8 + - + +
526A PHE* 3.9 24.0 - + + -
528A VAL* 3.4 26.7 - - + -
605A ILE* 4.7 2.9 - - + -
606A GLN 3.0 17.5 - - - +
607A MET* 4.0 6.3 - - + -
608A LEU* 3.9 11.5 - - - +
678A VAL* 3.2 43.1 - - + -
702A GLY* 1.3 82.0 - - - +
704A PHE* 1.3 75.3 + - - +
705A LEU* 4.4 15.9 - - + -
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Residues in contact with PHE 704 (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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480A HIS* 4.4 9.6 - + - -
484A ALA* 5.3 3.1 - - + -
485A ILE 3.4 6.3 - - - +
486A GLU* 3.1 42.4 - - + -
488A ARG* 3.5 15.0 - - - -
604A ARG 3.4 3.6 - - - +
605A ILE* 3.5 4.2 - - - -
606A GLN* 2.8 41.0 + - + +
608A LEU* 3.1 39.3 - - + -
703A PHE* 1.3 80.0 - - - +
705A LEU* 1.3 66.4 + - - +
706A ARG* 3.7 24.0 - - + -
697B VAL* 4.7 4.9 - - + -
698B GLY* 4.0 31.2 - - - -
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Residues in contact with LEU 705 (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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360A VAL* 4.5 1.8 - - + -
363A ILE* 3.8 19.1 - - + -
484A ALA* 3.0 6.1 - - - -
485A ILE* 2.7 48.4 + - + +
487A ILE* 5.6 0.7 - - + -
528A VAL* 3.7 27.6 - - + -
530A LEU* 3.7 25.8 - - + -
603A TYR* 3.2 20.7 - - + -
604A ARG 3.5 2.7 - - - +
605A ILE* 3.7 26.9 - - + -
678A VAL* 6.5 0.2 - - + -
703A PHE* 4.4 14.8 - - + -
704A PHE* 1.3 80.2 - - - +
706A ARG* 1.3 59.0 + - - +
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Residues in contact with ARG 706 (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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484A ALA* 3.7 19.7 - - + -
586A TYR* 4.8 0.6 + - - -
603A TYR* 3.1 8.5 - - - -
604A ARG* 2.9 72.9 + - + +
606A GLN* 3.5 22.8 + - - +
704A PHE* 3.7 27.1 - - - -
705A LEU* 1.3 71.8 - - - +
707A PRO* 1.3 72.7 - - + +
687B HIS* 5.1 5.8 + - + -
695B VAL* 4.5 5.3 - - - +
697B VAL* 2.8 39.1 + - + +
699B ASN* 3.0 28.2 + - - +
1750B CU 3.6 15.9 - - - -
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Residues in contact with PRO 707 (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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482A SER* 3.7 21.8 - - - +
483A GLY 3.1 23.6 - - - +
484A ALA* 3.9 4.9 - - + +
602A GLY 3.9 0.4 - - - +
603A TYR* 3.5 18.3 - - + -
604A ARG* 5.5 0.3 - - - +
706A ARG* 1.3 90.8 - - + +
708A TYR* 1.3 58.7 + - - +
710A PHE* 4.3 2.2 - - + -
711A PHE* 3.3 31.4 - - + -
687B HIS* 3.6 8.0 + - - -
689B GLU* 3.2 26.5 - - + +
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Residues in contact with TYR 708 (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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542A GLU* 2.9 24.0 + - - -
566A ARG* 4.6 1.6 - - - -
586A TYR* 3.1 37.6 - + - -
588A TYR* 3.8 38.6 - + + -
600A PRO 3.8 1.5 - - - +
602A GLY 2.8 32.7 + - - +
603A TYR 4.8 0.2 - - - -
604A ARG* 4.4 14.4 - - + +
706A ARG 4.1 5.6 - - - +
707A PRO* 1.3 73.8 - - - +
709A ASN* 1.3 90.1 + - + +
710A PHE 2.9 3.3 - - - +
509B ASN* 3.4 7.3 + - - -
685B ILE* 3.3 20.4 - - - +
687B HIS* 3.4 26.9 - + - -
689B GLU* 3.3 1.3 - - - -
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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