Contacts of the strand formed by residues 700 - 708 (chain B) 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 GLY 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488B ARG* 3.2 28.7 + - - -
489B PHE 3.6 4.9 - - - -
490B TYR* 3.4 30.5 - - - -
608B LEU* 5.0 1.0 - - - +
696B THR 3.5 4.6 + - - -
698B GLY 3.2 6.1 - - - +
699B ASN* 1.3 77.6 - - - +
701B VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 701 (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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488B ARG* 3.2 8.0 - - - -
489B PHE* 3.0 58.7 + - + +
608B LEU* 3.0 26.2 - - + +
610B PHE* 3.8 30.7 - - + -
680B ALA* 4.1 3.8 - - + -
681B GLY 4.0 22.0 - - - +
682B PHE* 4.0 19.1 - - + -
699B ASN 3.5 3.8 + - - +
700B GLY* 1.3 74.9 - - - +
702B GLY* 1.3 56.3 + - - +
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Residues in contact with GLY 702 (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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487B ILE* 3.1 12.3 - - - -
488B ARG* 4.4 0.9 - - - -
526B PHE* 5.6 3.1 - - - -
607B MET* 3.7 2.9 - - - +
608B LEU* 3.0 29.2 + - - +
678B VAL* 4.9 0.5 - - - +
680B ALA* 4.0 17.3 - - - +
701B VAL* 1.3 81.1 - - - +
703B PHE* 1.3 74.2 + - - +
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Residues in contact with PHE 703 (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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363B ILE* 4.7 3.1 - - + -
486B GLU* 3.6 4.3 - - - +
487B ILE* 3.0 63.0 + - + +
526B PHE* 3.8 28.7 - + + -
528B VAL* 4.1 26.5 - - + -
605B ILE* 5.0 3.4 - - + -
606B GLN 3.1 15.0 - - - +
607B MET* 3.9 12.6 - - + +
608B LEU* 4.1 7.7 - - - +
678B VAL* 3.6 32.8 - - + -
680B ALA* 5.4 0.4 - - + -
702B GLY* 1.3 82.4 - - - +
704B PHE* 1.3 70.2 + - - +
705B LEU* 4.1 25.8 - - + -
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Residues in contact with PHE 704 (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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697A VAL* 4.0 25.4 - - + -
698A GLY* 3.8 22.9 - - - -
480B HIS* 4.1 2.5 - + - -
484B ALA* 5.1 1.8 - - + -
485B ILE 3.4 8.3 - - - -
486B GLU* 3.4 48.0 - - + -
488B ARG* 4.4 2.9 - - - -
604B ARG 3.3 4.2 - - - +
605B ILE* 3.4 4.7 - - - -
606B GLN* 2.6 46.7 + - + +
608B LEU* 4.0 31.0 - - + -
703B PHE* 1.3 80.0 - - - +
705B LEU* 1.3 66.7 + - - +
706B ARG* 3.7 23.1 - - + -
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Residues in contact with LEU 705 (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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360B VAL* 4.3 11.9 - - + -
363B ILE* 3.5 32.5 - - + -
484B ALA* 3.1 5.4 - - - +
485B ILE* 2.8 55.8 + - + +
528B VAL* 3.9 22.2 - - + -
530B LEU* 4.3 11.2 - - + -
603B TYR* 3.6 17.6 - - + -
604B ARG 3.4 3.8 - - - +
605B ILE* 4.2 19.7 - - + -
703B PHE* 4.1 15.9 - - + -
704B PHE* 1.3 82.7 - - - +
706B ARG* 1.3 61.7 + - - +
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Residues in contact with ARG 706 (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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687A HIS* 5.2 2.0 + - - -
697A VAL* 3.2 16.0 + - - -
698A GLY 3.2 9.1 + - - -
699A ASN* 2.9 36.8 + - - +
1745A CU 3.8 14.5 - - - -
484B ALA* 4.2 9.6 - - + -
586B TYR* 4.8 0.4 + - - -
603B TYR* 3.4 4.6 - - - -
604B ARG* 2.6 74.8 + - + +
606B GLN* 2.9 31.2 + - + -
704B PHE* 3.7 24.5 - - + +
705B LEU* 1.3 77.2 - - - +
707B PRO* 1.3 72.7 - - + +
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Residues in contact with PRO 707 (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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687A HIS* 3.7 13.0 - - - -
689A GLU* 3.1 33.6 - - + +
482B SER* 3.8 17.3 - - - +
483B GLY 3.8 10.5 - - - +
484B ALA* 4.1 3.8 - - + +
602B GLY 3.7 5.8 - - - +
603B TYR* 3.4 30.5 - - + +
604B ARG* 5.6 0.3 - - - +
706B ARG* 1.3 89.7 - - + +
708B TYR* 1.3 59.5 + - - +
710B PHE* 3.9 1.1 - - + -
711B PHE* 3.5 20.2 - - + -
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Residues in contact with TYR 708 (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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509A ASN* 3.0 22.8 + - - -
685A ILE* 3.1 13.7 - - - +
687A HIS* 3.5 28.9 - + - -
689A GLU* 3.8 1.8 - - - -
542B GLU* 2.6 37.5 + - - -
586B TYR* 3.2 33.9 - + - -
588B TYR* 4.0 25.1 - + + -
600B PRO 3.8 1.3 - - - +
602B GLY* 2.9 31.6 + - - +
604B ARG* 4.5 11.9 - - + +
706B ARG 3.6 4.2 + - - +
707B PRO* 1.3 74.7 - - - +
709B ASN* 1.3 94.4 + - - +
710B PHE 3.0 2.2 - - - -
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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