Contacts of the helix formed by residues 687 - 691 (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 HIS 687 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A TYR* 4.3 2.1 + + - -
604A ARG* 5.7 1.6 - - - -
706A ARG* 5.1 6.4 + - - -
707A PRO 3.6 9.6 + - - -
708A TYR* 3.4 23.2 - + + -
709A ASN* 3.3 24.2 - - - +
509B ASN* 4.3 0.4 - - - +
511B VAL* 4.0 12.6 - - - +
685B ILE 3.3 22.2 - - - -
686B PRO* 1.3 75.8 - - - +
688B ALA* 1.3 69.9 + - - +
689B GLU* 2.9 42.2 + - + +
690B ASP* 2.7 36.2 + - - +
695B VAL* 6.3 2.5 - - + -
1750B CU 2.5 27.5 - - - -
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Residues in contact with ALA 688 (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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595A ASN* 3.7 11.2 - - - +
597A TRP* 4.4 5.4 - - + -
709A ASN* 3.3 6.7 + - - +
711A PHE 2.9 31.0 - - - +
712A ASP* 3.6 16.2 - - - +
713A GLU* 3.2 9.7 - - - -
511B VAL* 4.3 10.5 - - - +
687B HIS* 1.3 71.8 - - - +
689B GLU* 1.3 56.8 + - - +
690B ASP 2.7 12.0 + - - -
691B ILE* 2.9 25.4 + - - +
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Residues in contact with GLU 689 (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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482A SER 5.7 0.2 - - - +
707A PRO* 3.2 28.0 - - + +
708A TYR 3.2 0.2 - - - -
709A ASN* 2.3 35.0 + - - -
710A PHE 3.7 0.7 + - - -
711A PHE* 3.1 42.4 + - + +
713A GLU 3.6 1.5 - - - +
714A ASP* 3.5 31.9 - - - +
715A PRO* 4.5 2.7 - - + -
687B HIS* 2.9 29.2 + - + +
688B ALA* 1.3 69.1 - - - +
690B ASP* 1.3 60.5 + - - +
691B ILE 3.2 3.8 - - - -
693B ASN 3.7 7.8 - - - +
695B VAL* 4.7 11.8 + - + +
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Residues in contact with ASP 690 (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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493B GLY 4.7 0.2 - - - +
495B ILE* 4.3 18.9 - - + +
684B HIS* 2.8 29.3 + - - -
686B PRO* 3.2 2.9 - - - +
687B HIS* 2.7 50.5 + - - +
689B GLU* 1.3 75.3 - - - +
691B ILE* 1.3 57.1 + - + +
692B PRO 2.7 22.9 - - - +
693B ASN* 3.2 17.7 - - - -
694B THR* 3.6 26.0 + - - +
695B VAL* 4.8 2.1 + - - +
1750B CU 3.8 2.8 - - - -
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Residues in contact with ILE 691 (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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712A ASP 5.1 0.2 - - - +
713A GLU* 3.5 12.3 - - + +
714A ASP* 2.6 33.8 + - - +
240B LEU* 4.0 23.6 - - + -
298B GLY* 3.8 1.3 - - - -
299B SER* 3.5 35.4 - - - +
495B ILE* 4.2 6.1 - - + -
511B VAL* 3.5 47.1 - - + +
512B SER* 5.4 1.8 - - - +
688B ALA 2.9 15.0 + - - +
689B GLU 3.2 0.2 - - - -
690B ASP* 1.3 88.3 - - - +
692B PRO* 1.3 69.0 - - + +
693B ASN 3.6 0.7 - - - -
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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