Contacts of the helix formed by residues 835 - 839 (chain A) in PDB entry 3IAY
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 LEU 835 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811A ILE* 4.5 12.8 - - + -
815A ARG* 3.9 20.0 - - + +
816A TYR* 3.7 33.2 - - - +
817A ALA* 4.1 8.5 - - + -
832A GLN* 3.9 18.6 - - + +
833A LYS 2.9 12.9 + - - +
834A GLY* 1.3 81.5 - - - +
836A ALA* 1.3 66.5 + - - +
837A SER* 2.9 13.9 - - - +
838A VAL* 2.8 19.4 + - + +
839A ARG 3.4 3.6 + - - -
850A MET* 3.9 11.4 - - + -
854A LEU* 4.0 16.2 - - + -
968A SER* 5.9 1.6 - - - +
969A ILE* 4.6 11.2 - - + -
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Residues in contact with ALA 836 (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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815A ARG* 4.5 7.6 - - - +
834A GLY 3.8 0.4 + - - -
835A LEU* 1.3 73.8 - - - +
837A SER* 1.3 59.9 + - - +
839A ARG* 3.1 22.5 + - - +
842A SER* 2.4 36.7 + - - +
846A VAL* 4.2 9.4 - - + -
847A SER* 3.5 0.8 + - - -
850A MET* 3.7 19.5 - - + +
965A PRO* 4.5 13.0 - - + -
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Residues in contact with SER 837 (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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832A GLN* 2.1 29.5 + - - -
835A LEU* 3.7 2.1 - - - +
836A ALA* 1.3 79.1 - - - +
838A VAL* 1.3 60.4 + - - +
839A ARG 3.6 0.2 - - - -
847A SER* 3.7 25.6 + - - +
850A MET* 3.6 30.3 - - - +
851A ASN* 3.3 27.9 + - - +
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Residues in contact with VAL 838 (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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832A GLN* 3.7 38.1 - - + +
834A GLY* 3.6 26.7 - - - +
835A LEU 2.8 16.9 + - - +
837A SER* 1.3 82.6 - - - +
839A ARG* 1.3 62.7 + - - +
840A ARG* 5.0 2.2 - - - +
851A ASN* 5.7 0.2 - - - +
10P T 3.6 18.1 + - - +
11P A 4.0 9.2 - - - +
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Residues in contact with ARG 839 (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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475A ARG* 4.4 6.5 + - - -
815A ARG* 3.9 15.1 - - - +
834A GLY 3.6 17.4 + - - +
835A LEU 3.6 10.1 - - - +
836A ALA* 3.1 23.2 + - - +
837A SER 5.1 0.2 - - - -
838A VAL* 1.3 79.2 - - - +
840A ARG* 1.3 62.7 + - - +
841A ASP* 3.0 34.0 + - - +
842A SER* 3.2 16.2 + - - +
847A SER* 4.6 0.7 + - - -
8P C 3.0 24.7 + - - -
9P C 3.0 40.2 + - - +
10P T 3.7 22.1 + - - -
8T G 4.4 2.0 - - - +
9T G 3.2 15.9 - - - +
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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