Contacts of the strand formed by residues 485 - 493 (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 ILE 485 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A TRP* 3.3 36.6 - - + -
352A VAL* 3.5 17.7 - - + -
359A LEU* 4.1 10.3 - - + -
360A VAL* 4.1 21.1 - - + -
363A ILE* 4.6 9.0 - - + -
477A THR* 4.3 12.1 - - - +
478A VAL 3.6 5.4 - - - +
479A PHE* 3.8 21.8 - - + -
484A ALA* 1.3 73.0 - - - +
486A GLU* 1.3 62.8 + - - +
487A ILE* 4.2 8.4 + - + +
603A TYR* 5.2 0.9 - - + -
703A PHE 4.1 0.3 - - - +
704A PHE* 3.4 2.3 - - - -
705A LEU* 2.7 52.1 + - + +
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Residues in contact with GLU 486 (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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476A ASP* 5.7 0.2 - - - +
477A THR* 3.0 5.0 + - - -
478A VAL* 2.7 52.6 + - + +
480A HIS* 3.2 29.9 + - - +
484A ALA 4.0 0.6 + - - -
485A ILE* 1.3 73.8 - - - +
487A ILE* 1.3 67.6 + - - +
488A ARG* 2.7 46.7 + - + +
490A TYR* 5.3 0.2 + - - -
703A PHE 3.5 7.2 - - - +
704A PHE* 3.1 37.0 - - + -
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Residues in contact with ILE 487 (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* 4.2 22.0 - - + -
476A ASP 3.8 7.4 - - - +
477A THR* 3.2 32.1 - - - +
485A ILE* 4.6 11.9 - - + +
486A GLU* 1.3 79.6 - - - +
488A ARG* 1.3 64.4 + - - +
526A PHE* 3.7 36.3 - - + -
702A GLY* 2.9 25.1 - - - -
703A PHE* 2.9 48.2 + - + +
705A LEU* 5.6 0.4 - - + -
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Residues in contact with ARG 488 (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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476A ASP* 2.7 49.1 + - + +
486A GLU* 2.7 45.0 + - + +
487A ILE* 1.3 79.9 - - - +
489A PHE* 1.3 58.2 + - - +
490A TYR* 3.7 30.6 + - + +
608A LEU* 3.4 28.2 - - + +
700A GLY* 3.2 28.5 + - - -
701A VAL 3.4 7.4 - - - +
702A GLY 4.6 0.7 - - - +
704A PHE* 3.5 15.0 - - - -
488B ARG* 5.1 11.1 - - - +
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Residues in contact with PHE 489 (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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473A TYR* 3.9 23.8 - + - -
474A VAL 3.0 6.1 - - - -
475A TRP* 3.1 39.7 - + + -
488A ARG* 1.3 75.4 - - - +
490A TYR* 1.3 76.2 + - - +
491A ALA* 4.6 4.3 - - + -
522A HIS* 4.9 12.8 - - + -
523A SER 4.6 4.5 - - - -
524A ALA* 3.4 25.6 - - + -
526A PHE* 3.8 20.9 - + + -
680A ALA 3.8 9.2 - - - -
682A PHE* 5.0 4.7 - + - -
699A ASN 4.0 1.2 - - - +
700A GLY* 3.5 0.7 - - - -
701A VAL* 2.9 59.8 + - + +
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Residues in contact with TYR 490 (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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473A TYR* 3.2 6.9 - - - -
474A VAL* 2.9 45.2 + - + -
476A ASP* 3.7 22.1 + - - -
486A GLU* 5.3 0.2 + - - -
488A ARG* 3.7 36.1 + - + +
489A PHE* 1.3 86.5 - - - +
491A ALA* 1.3 60.5 + - - +
492A THR 4.2 0.2 - - - -
696A THR* 3.4 43.1 - - + -
697A VAL* 5.9 0.2 - - - -
698A GLY* 5.4 2.0 - - - -
699A ASN 4.1 5.8 - - - +
700A GLY* 3.2 29.6 - - - -
438B LEU* 3.5 30.8 - - + +
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Residues in contact with ALA 491 (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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471A PAQ 4.9 4.9 - - + +
472A ASP 3.8 3.8 - - - -
473A TYR* 4.1 21.1 - - + -
489A PHE* 4.6 3.3 - - + -
490A TYR* 1.3 76.2 - - - +
492A THR* 1.3 60.8 + - - +
522A HIS* 4.2 29.2 - - + +
682A PHE* 4.7 11.0 - - + -
694A THR* 3.8 18.5 - - + +
695A VAL 4.6 4.9 - - - +
696A THR* 5.2 0.7 - - - -
699A ASN* 4.6 8.9 + - - +
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Residues in contact with THR 492 (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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471A PAQ 2.8 28.1 - - - +
472A ASP* 2.9 26.9 + - + +
474A VAL* 4.4 14.4 - - + -
491A ALA* 1.3 73.5 - - - +
493A GLY* 1.3 71.4 + - - +
494A TYR 4.0 0.7 - - - +
694A THR* 2.5 31.1 + - - -
696A THR* 4.4 13.7 - - + -
441B ARG* 3.7 3.1 - - - +
442B ARG* 3.1 39.5 + - + +
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Residues in contact with GLY 493 (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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472A ASP* 2.8 20.6 - - - -
492A THR* 1.3 86.4 + - - +
494A TYR* 1.3 58.1 + - - -
693A ASN* 2.8 39.2 + - - -
694A THR* 3.1 6.1 + - - -
442B ARG 3.1 8.5 + - - -
443B HIS* 3.7 4.3 - - - -
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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