Contacts of the helix formed by residues 708 - 716 (chain A) in PDB entry 6CIM
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 ASP 708 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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599A CYS 4.8 2.0 + - - -
600A ASP* 3.1 9.6 - - - +
662A GLU* 4.7 0.3 - - - +
707A TYR* 1.3 74.5 - - - +
709A GLU* 1.3 66.2 + - - +
710A LYS* 3.2 11.8 + - - +
711A LEU* 3.0 21.1 + - - +
712A VAL* 2.9 19.1 + - - +
958A SER* 5.2 14.6 - - - -
1102A MN 2.2 36.0 + - - -
32F A 5.1 4.4 + - - +
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Residues in contact with GLU 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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708A ASP* 1.3 74.9 - - - +
710A LYS* 1.3 65.1 + - - +
712A VAL* 3.2 7.9 + - - +
713A ARG* 2.7 66.9 + - + +
721A SER* 3.7 17.1 + - - +
726A ILE 4.1 1.3 - - - +
728A THR* 4.0 8.4 - - + +
934A ASN* 3.5 30.8 + - - +
935A TYR* 5.7 3.7 - - + -
938A LYS* 3.4 25.5 + - - +
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Residues in contact with LYS 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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661A ASP* 5.3 1.4 + - - -
662A GLU* 3.5 35.7 + - - +
663A SER* 3.3 26.4 + - - -
708A ASP* 3.2 10.1 + - - +
709A GLU* 1.3 78.6 - - - +
711A LEU* 1.3 58.2 + - - +
713A ARG* 3.4 6.9 + - - +
714A GLU* 3.0 34.5 + - - +
721A SER* 4.8 10.0 + - - +
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Residues in contact with LEU 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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599A CYS* 3.1 52.5 - - + +
600A ASP* 4.0 8.3 - - - +
601A GLY 4.9 0.2 - - - +
620A VAL* 5.7 0.4 - - + -
662A GLU* 3.9 28.3 - - + +
668A LEU* 4.2 23.6 - - + -
707A TYR* 4.1 14.8 - - + -
708A ASP* 3.0 16.6 + - - +
710A LYS* 1.3 76.3 - - + +
712A VAL* 1.3 67.1 + - - +
714A GLU* 3.7 11.4 - - + +
715A VAL* 2.9 33.8 + - + +
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Residues in contact with VAL 712 (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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704A GLY 6.0 0.2 - - - +
707A TYR* 3.5 27.1 - - + +
708A ASP 2.9 17.0 + - - +
709A GLU* 3.4 11.0 - - - +
711A LEU* 1.3 77.0 - - - +
713A ARG* 1.3 65.0 + - - +
715A VAL* 3.5 6.4 - - - +
716A GLU* 2.9 34.7 + - + +
718A LEU* 4.8 2.7 - - + -
728A THR* 4.1 27.4 - - + +
787A THR* 4.0 17.9 - - - +
789A PRO* 4.0 24.5 - - + -
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Residues in contact with ARG 713 (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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709A GLU* 2.7 63.0 + - + +
710A LYS* 3.7 5.6 - - - +
712A VAL* 1.3 72.9 - - - +
714A GLU* 1.3 64.2 + - - +
717A GLY 3.5 0.9 + - - -
718A LEU* 3.0 50.2 + - + +
719A GLU* 2.7 32.3 + - - +
720A ALA* 4.1 6.1 + - - +
721A SER* 3.7 30.7 + - - +
723A SER* 4.6 4.0 - - - -
725A TYR* 2.4 32.9 + - - +
726A ILE* 3.3 16.2 + - - +
727A CYS 4.8 1.8 + - - -
728A THR* 3.7 17.9 - - + +
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Residues in contact with GLU 714 (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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662A GLU 3.1 26.9 - - - +
663A SER* 3.7 20.5 + - - +
665A HIS* 2.7 51.6 + - + +
668A LEU* 4.5 8.5 - - + -
710A LYS* 3.0 25.1 + - + +
711A LEU* 3.7 11.7 - - + +
712A VAL 3.2 0.4 - - - -
713A ARG* 1.3 80.3 - - - +
715A VAL* 1.3 61.7 + - - +
716A GLU 3.5 0.2 + - - -
717A GLY* 3.7 6.8 + - - -
718A LEU 5.2 1.1 - - - -
782A LYS 5.5 1.4 - - - +
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Residues in contact with VAL 715 (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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668A LEU* 4.3 14.6 - - + -
672A LEU* 5.7 0.9 - - + -
707A TYR* 4.6 6.1 - - + -
711A LEU* 2.9 27.1 + - + +
712A VAL 3.5 4.7 - - - +
714A GLU* 1.3 77.1 - - - +
716A GLU* 1.3 56.8 + - - +
717A GLY 3.4 1.6 - - - -
783A PRO* 3.3 0.6 - - - +
784A PHE* 2.6 64.6 + - + -
785A ILE* 3.2 22.9 + - + -
787A THR* 3.8 27.6 - - + -
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Residues in contact with GLU 716 (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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712A VAL* 2.9 22.1 + - + +
714A GLU 3.4 0.2 - - - -
715A VAL* 1.3 74.5 - - - +
717A GLY* 1.3 60.5 + - - +
718A LEU* 3.3 21.5 + - + +
749A SER* 5.1 1.0 - - - -
750A HIS* 2.9 41.0 + - - +
753A ASN* 3.6 18.7 + - - +
779A VAL* 4.6 1.0 - - - +
783A PRO* 3.2 21.6 - - - +
785A ILE 3.3 13.9 - - - +
786A GLU* 4.5 0.6 - - - -
787A THR* 3.2 43.7 + - + +
789A PRO* 4.7 3.8 - - - +
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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