Contacts of the strand formed by residues 600 - 608 (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 PRO 600 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A TRP* 4.4 20.9 - - + +
566A ARG* 3.7 26.1 + - - +
588A TYR* 5.2 3.0 - - - +
590A ALA* 4.0 20.0 - - + +
591A SER 4.1 8.7 - - - +
592A ASN 5.0 3.1 - - - +
593A HIS 3.9 6.7 - - - +
594A SER* 4.1 7.2 - - - +
598A GLY 4.4 2.7 - - - +
599A HIS* 1.3 84.3 - - - +
601A ARG* 1.3 64.0 + - - +
602A GLY* 3.3 3.8 + - - -
708A TYR* 3.8 3.3 - - - +
709A ASN* 3.5 15.1 + - - +
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Residues in contact with ARG 601 (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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357A GLU* 3.1 24.9 + - - -
532A VAL* 2.9 8.3 - - + +
533A ALA* 3.3 26.5 - - - +
590A ALA* 4.1 0.2 - - - -
591A SER* 2.7 34.1 + - - +
593A HIS* 2.9 27.1 + - + +
594A SER 3.6 16.2 - - - -
595A ASN* 3.7 16.6 - - - +
600A PRO* 1.3 68.9 - - - +
602A GLY* 1.3 58.5 + - - +
709A ASN 3.3 7.4 - - - +
710A PHE* 2.4 57.6 + - + +
711A PHE* 4.8 2.0 - - - +
712A ASP* 6.0 0.2 + - - -
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Residues in contact with GLY 602 (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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532A VAL* 3.8 4.9 - - - -
588A TYR* 4.5 4.0 - - - -
589A LEU 3.2 12.6 - - - -
590A ALA* 3.8 5.2 - - - -
600A PRO 3.3 2.0 + - - -
601A ARG* 1.3 75.5 - - - +
603A TYR* 1.3 65.3 - - - -
708A TYR* 2.8 41.7 + - - +
710A PHE* 3.3 11.3 - - - +
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Residues in contact with TYR 603 (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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359A LEU* 3.1 39.1 - - + +
483A GLY* 2.4 36.2 + - - -
484A ALA* 4.7 0.2 - - - -
485A ILE* 5.0 1.8 - - + -
530A LEU* 4.2 24.2 - - + +
532A VAL* 4.4 7.8 - - + +
588A TYR* 2.7 22.7 - - - +
589A LEU* 2.8 20.0 + - - +
602A GLY* 1.3 82.2 - - - -
604A ARG* 1.3 56.4 + - - +
605A ILE* 4.8 2.4 - - - +
705A LEU* 3.2 31.0 - - + -
706A ARG 3.1 15.3 - - - -
707A PRO* 3.5 15.5 - - + +
710A PHE* 3.6 30.5 - + - -
711A PHE* 4.2 5.0 - - - -
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Residues in contact with ARG 604 (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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585A ARG* 2.8 31.3 + - - +
586A TYR* 3.3 51.4 + - + +
587A LEU 3.2 10.8 + - - +
588A TYR* 3.0 16.2 - - + -
603A TYR* 1.3 75.7 - - - +
605A ILE* 1.3 62.8 + - - +
606A GLN* 4.6 30.8 - - - +
704A PHE 3.4 4.5 - - - +
705A LEU* 3.5 3.8 - - - +
706A ARG* 2.9 73.2 + - + +
707A PRO 5.8 0.4 - - - -
708A TYR* 4.4 10.8 - - + +
683B LEU 5.3 0.6 + - - -
687B HIS* 5.7 1.6 - - - -
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Residues in contact with ILE 605 (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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528A VAL* 5.7 1.8 - - + -
530A LEU* 4.8 6.5 - - + -
585A ARG 5.7 0.9 - - - +
587A LEU* 2.8 23.7 + - + +
588A TYR* 5.2 1.6 - - - -
589A LEU* 4.7 18.8 - - + +
603A TYR 4.8 3.8 - - - +
604A ARG* 1.3 76.2 + - - +
606A GLN* 1.3 61.5 + - - +
607A MET* 3.5 18.2 + - + +
632A LEU* 4.3 19.5 - - + +
634A VAL* 5.9 0.4 - - + -
676A ALA* 3.8 29.8 - - + -
678A VAL* 4.2 22.2 - - + -
703A PHE* 4.7 4.3 - - + -
704A PHE 3.5 5.8 - - - +
705A LEU* 3.7 20.6 - - + -
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Residues in contact with GLN 606 (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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604A ARG* 3.8 30.2 + - - +
605A ILE* 1.3 70.7 - - - +
607A MET* 1.3 69.7 + - - +
608A LEU* 4.2 9.6 - - + -
703A PHE* 3.0 5.9 - - - +
704A PHE* 2.8 47.5 + - + +
706A ARG* 3.5 28.3 + - - +
610B PHE* 3.0 36.5 - - + -
682B PHE* 6.3 0.6 - - - -
698B GLY* 3.4 26.1 + - - +
699B ASN* 5.5 0.8 + - - -
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Residues in contact with MET 607 (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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583A THR* 6.0 3.8 - - - -
605A ILE* 3.5 15.5 + - + +
606A GLN* 1.3 81.5 - - - +
608A LEU* 1.3 69.7 + - - +
609A SER* 3.5 20.0 - - - +
631A GLN* 3.7 42.2 - - + +
632A LEU* 4.2 14.1 - - - -
678A VAL* 4.0 19.1 - - + -
679A THR 3.3 26.5 - - - +
702A GLY 5.4 0.4 - - - +
703A PHE* 4.0 2.9 - - + -
610B PHE* 4.3 10.7 - - - -
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Residues in contact with LEU 608 (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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488A ARG* 3.4 29.8 - - + +
606A GLN* 4.2 10.5 - - + -
607A MET* 1.3 91.5 - - - +
609A SER* 1.3 59.7 + - - +
610A PHE* 4.7 5.6 - - + -
701A VAL* 3.2 13.4 - - + +
702A GLY 3.1 29.3 + - - +
703A PHE* 3.9 17.0 - - - +
704A PHE* 3.1 41.7 - - + -
610B PHE* 4.3 16.2 - - + -
698B GLY 5.9 0.4 - - - +
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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