Contacts of the helix formed by residues 670 - 674 (chain I) in PDB entry 6C6S
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 PHE 670 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669I PRO* 1.3 75.3 - - + +
671I LEU* 1.3 63.4 + - - +
672I GLU* 3.2 15.3 + - - -
673I HIS* 3.3 33.0 + + + +
674I ASP* 3.7 12.6 - - - +
700I VAL* 4.4 9.6 - - + -
1110I GLY* 3.8 14.1 - - - +
1113I LEU* 3.4 39.5 - - + -
1114I GLU* 3.5 25.8 - - + -
1117I LEU* 3.6 28.0 - - + -
1184I THR* 3.5 21.5 - - + +
1185I PRO 4.7 6.7 + - - -
1186I VAL 4.7 0.2 + - - -
1190I ALA 3.6 19.3 - - - -
1195I ILE* 3.9 7.0 - - + -
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Residues in contact with LEU 671 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561I ILE* 3.8 17.9 - - + -
661I VAL* 4.2 6.7 - - + -
665I ALA 3.3 26.0 - - - +
668I ILE* 3.7 30.9 + - + +
669I PRO 3.2 2.3 - - - -
670I PHE* 1.3 78.0 - - - +
672I GLU* 1.3 62.9 + - - +
673I HIS 3.1 1.6 + - - -
674I ASP* 3.2 15.2 + - + +
679I ALA* 3.7 30.3 - - + -
1186I VAL* 3.7 26.5 + - + +
1187I PHE* 4.1 9.9 - - + -
772J TYR* 3.7 15.9 + - - +
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Residues in contact with GLU 672 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670I PHE* 3.3 11.0 - - - -
671I LEU* 1.3 80.4 + - - +
673I HIS* 1.3 87.8 + - + +
674I ASP 3.5 0.9 - - - -
1185I PRO 4.7 0.3 - - - +
1186I VAL 2.8 20.2 - - - +
1187I PHE* 3.5 29.2 - - + +
1189I GLY* 4.3 17.2 + - - -
1190I ALA 4.8 1.4 - - - +
766J GLY* 3.7 15.3 - - - -
767J LEU* 3.3 52.7 + - - +
772J TYR* 4.7 5.2 - - - -
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Residues in contact with HIS 673 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670I PHE* 3.3 28.1 + + + +
671I LEU 3.1 1.0 - - - -
672I GLU* 1.3 110.7 + - - +
674I ASP* 1.3 61.0 + - - +
1107I MET 4.5 0.2 - - - +
1109I ILE* 3.2 29.0 + - + +
1110I GLY* 4.0 6.7 - - - -
1113I LEU* 3.7 22.6 - - + +
1190I ALA 4.9 3.6 + - - -
1191I LYS* 6.2 0.2 - - - -
1192I GLU* 6.2 0.9 - - + -
763J PHE* 2.7 40.4 + - - +
764J ARG 3.8 9.2 + - - -
765J GLU 3.3 25.6 + - - -
766J GLY* 3.5 7.8 - - - -
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Residues in contact with ASP 674 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668I ILE* 4.6 7.3 - - - +
670I PHE 3.7 8.8 - - - +
671I LEU* 3.2 10.0 + - - +
673I HIS* 1.3 80.9 - - - +
675I ASP* 1.3 71.7 + - - +
678I ARG* 5.2 0.2 - - + -
679I ALA* 4.7 11.6 - - + +
1070I HIS* 2.8 31.7 + - - +
1107I MET 3.9 2.5 - - - -
1108I ASN* 3.3 19.8 - - + +
1110I GLY* 2.8 28.4 + - - -
763J PHE* 3.6 9.5 - - - -
772J TYR* 3.1 22.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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