Contacts of the helix formed by residues 706 - 711 (chain A) in PDB entry 4BSN
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 706 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ILE* 5.4 4.5 - - + -
658A MET* 3.6 27.6 - - + -
695A ASN* 3.2 31.9 - - - -
698A ALA 4.2 5.8 - - - -
699A CYS* 3.8 43.5 - - + -
702A VAL* 4.8 8.7 - - + -
703A GLY 3.5 15.0 - - - +
704A HIS 2.5 11.1 + - - +
705A PRO* 1.3 72.1 - - - +
707A VAL* 1.3 55.9 + - - -
708A ILE* 3.2 4.5 - - - -
709A GLN* 3.2 14.6 + - + +
710A LEU* 2.9 55.1 + - + +
713A ILE* 5.6 3.1 - - + -
762A TRP* 4.0 10.5 - + + -
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Residues in contact with VAL 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A GLU* 5.9 5.8 - - + -
704A HIS* 4.0 13.2 - - + +
705A PRO* 4.5 9.0 - - + -
706A PHE* 1.3 81.5 - - - +
708A ILE* 1.3 63.2 + - + +
710A LEU* 4.2 7.2 - - + -
711A GLY* 3.0 27.4 + - - -
762A TRP* 3.4 36.8 - - + +
771A MET* 4.2 13.5 - - + -
776A PHE* 5.5 5.1 - - + -
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Residues in contact with ILE 708 (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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651A GLU* 4.1 54.7 - - + +
654A ILE* 4.4 16.6 - - + -
655A GLU* 5.4 11.2 - - + +
705A PRO 4.5 10.8 - - - +
706A PHE 4.7 0.9 - - - -
707A VAL* 1.3 83.3 - - + +
709A GLN* 1.3 63.4 + - + +
711A GLY* 4.4 1.4 + - - -
712A ARG* 3.9 16.5 + - - +
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Residues in contact with GLN 709 (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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654A ILE* 4.8 5.5 + - + -
655A GLU* 4.7 16.6 + - - +
658A MET* 3.6 42.9 + - + +
659A LEU* 6.1 0.4 - - - +
662A ASN* 3.0 37.9 + - - +
706A PHE* 3.2 20.2 + - + +
708A ILE* 1.3 85.4 + - + +
710A LEU* 1.3 65.4 + - - +
711A GLY 3.4 0.4 - - - -
712A ARG* 3.2 36.7 - - - +
713A ILE* 3.4 15.5 - - + +
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Residues in contact with LEU 710 (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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699A CYS* 6.1 0.4 - - - -
706A PHE* 2.9 37.7 + - + +
707A VAL* 4.1 2.2 - - - +
709A GLN* 1.3 76.7 - - - +
711A GLY* 1.3 58.1 + - - +
713A ILE* 3.5 13.1 + - + +
714A TYR* 3.0 31.8 + - + +
717A MET* 5.2 11.2 - - + -
758A LEU* 5.1 14.1 - - + +
759A ILE* 5.8 3.4 - - - +
762A TRP* 3.4 53.6 - - + -
776A PHE* 4.3 19.1 - - + -
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Residues in contact with GLY 711 (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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707A VAL 3.0 17.3 + - - -
708A ILE 5.0 0.4 - - - -
709A GLN 3.4 0.2 - - - -
710A LEU* 1.3 78.4 - - - +
712A ARG* 1.3 61.3 + - - +
714A TYR* 3.4 18.4 + - - +
715A LEU* 4.5 2.4 + - - +
776A PHE* 4.5 13.0 - - - -
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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