Contacts of the helix formed by residues 798 - 803 (chain A) in PDB entry 5C51
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 798 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A TYR* 3.7 37.0 - - + +
455A LEU* 3.8 26.0 - - + -
456A GLN* 4.8 10.5 - - + -
459A MET* 4.6 22.2 - - + -
794A ILE* 3.3 22.0 + - + +
795A ASN* 3.9 0.7 - - - +
797A MET* 1.3 74.4 - - - +
799A SER* 1.3 64.1 + - - +
800A PHE 3.3 2.7 - - - -
801A TRP* 4.0 3.6 - - - +
802A ARG* 3.1 44.6 + - - +
870A VAL* 3.8 18.8 - - + -
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Residues in contact with SER 799 (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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595A GLN* 5.1 0.2 + - - -
795A ASN* 2.3 38.6 + - - -
796A LYS* 3.3 10.6 - - - -
797A MET 3.3 2.6 - - - -
798A ILE* 1.3 78.9 - - - +
800A PHE* 1.3 62.1 + - - +
802A ARG* 3.3 21.7 + - - +
803A ASN* 3.6 17.0 + - - -
869A ARG* 3.4 16.8 - - - -
21P G 3.9 25.8 + - - +
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Residues in contact with PHE 800 (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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797A MET 4.5 1.5 + - - +
798A ILE 3.3 0.4 - - - -
799A SER* 1.3 74.5 - - - +
801A TRP* 1.3 74.1 + + - +
802A ARG 3.1 1.6 - - - -
803A ASN* 3.1 13.1 + - - +
804A ALA* 3.4 33.2 - - + +
807A ARG* 5.1 3.1 - - - -
808A ILE* 5.1 7.0 - - + -
861A THR 3.8 13.2 - - - -
862A ALA* 4.5 3.4 - - - -
863A SER* 3.6 39.9 - - - -
869A ARG* 3.1 34.2 - - + +
870A VAL 5.6 0.2 - - - +
871A GLY* 3.3 38.6 - - - +
872A SER* 4.7 0.4 - - - -
874A LEU* 4.9 8.7 - - + -
21P G 5.3 3.8 - - + -
22P T 4.4 13.0 - - - -
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Residues in contact with TRP 801 (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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444A TYR* 3.2 30.1 - + - -
445A LEU* 4.5 11.0 - - + -
448A ALA* 3.5 26.2 - - + -
449A GLN* 3.0 32.4 + - + +
452A TYR* 3.4 41.3 - + + +
797A MET 5.2 0.6 + - - -
798A ILE* 3.6 5.3 + - - +
800A PHE* 1.3 83.4 - + - +
802A ARG* 1.3 63.8 + - - +
803A ASN 3.3 0.2 - - - -
804A ALA* 4.0 1.6 - - - -
805A HIS* 3.1 52.2 + - + +
808A ILE* 4.1 28.9 - - + -
809A SER* 5.8 3.1 - - - -
870A VAL* 4.4 16.8 - - + -
871A GLY* 3.5 22.0 - - - +
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Residues in contact with ARG 802 (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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452A TYR* 3.8 24.4 + - + +
459A MET* 5.9 1.8 - - - -
594A LEU* 4.7 10.1 + - - +
595A GLN* 3.0 37.7 + - - +
795A ASN* 3.3 22.0 + - - +
798A ILE* 3.1 37.5 + - - +
799A SER* 3.3 29.7 + - - +
800A PHE 3.1 0.4 - - - -
801A TRP* 1.3 79.3 - - - +
803A ASN* 1.3 73.1 + - - +
804A ALA 3.4 0.6 + - - -
805A HIS* 3.4 17.3 + - - -
21P G 5.4 2.6 - - - -
10T G 3.7 11.8 - - - +
11T C 4.0 27.2 + - - +
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Residues in contact with ASN 803 (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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799A SER 3.6 11.8 + - - +
800A PHE* 3.1 8.1 + - - +
802A ARG* 1.3 101.0 - - - +
804A ALA* 1.3 59.0 + - - +
807A ARG* 3.0 23.4 + - - -
20P C 4.7 1.6 + - - -
21P G 3.3 32.1 + - - +
9T G 3.8 14.1 + - - +
10T G 3.5 45.2 + - - +
11T C 4.3 1.2 - - - +
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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