Contacts of the strand formed by residues 696 - 702 (chain H) in PDB entry 6C3P
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 696 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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684H GLY 3.9 1.1 - - - -
685H TYR* 3.1 4.3 - - - +
686H PHE* 2.7 71.6 + - + +
694H PRO* 4.0 2.1 - - - +
695H THR* 1.3 85.3 - - + +
697H SER* 1.3 67.1 + - - +
699H ILE* 4.3 12.8 - - + -
718H GLY* 4.3 14.1 - - - +
721H SER 4.2 5.2 - - - +
722H LEU* 3.4 42.0 - - + +
725H ALA* 4.4 0.2 - - + -
730H MET* 4.5 1.3 - - - -
902H MET* 5.6 2.2 - - - -
905H GLY* 3.4 28.0 - - - +
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Residues in contact with SER 697 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684H GLY 3.3 0.4 + - - -
685H TYR* 3.4 17.7 - - - -
694H PRO* 3.7 26.3 + - - +
695H THR 4.2 0.8 + - - -
696H LEU* 1.3 79.5 + - - +
698H ASN* 1.3 74.1 + - - +
699H ILE* 3.5 1.5 - - - +
905H GLY 3.9 5.9 + - - -
906H THR* 4.0 20.4 + - - +
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Residues in contact with ASN 698 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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683H GLY* 3.8 21.4 - - - -
684H GLY 2.6 11.3 + - - -
685H TYR* 3.4 24.5 + - + +
697H SER* 1.3 75.9 - - - +
699H ILE* 1.3 57.0 + - - +
700H THR* 4.3 7.1 + - - -
906H THR* 4.4 6.3 - - + +
907H ILE* 4.2 10.9 - - - +
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Residues in contact with ILE 699 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681H ILE* 3.6 20.9 - - + +
683H GLY 3.2 5.2 + - - -
684H GLY* 2.5 41.0 + - - +
686H PHE* 3.5 27.8 - - + -
696H LEU* 4.3 14.4 - - + -
697H SER 4.2 6.5 - - - +
698H ASN* 1.3 80.6 - - - +
700H THR* 1.3 59.4 + - - +
701H ILE* 3.8 6.3 - - + -
722H LEU* 3.6 23.3 - - + -
902H MET* 6.3 0.9 - - + -
905H GLY 4.3 12.3 - - - +
906H THR* 4.4 0.4 - - - -
907H ILE* 4.1 33.2 - - + +
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Residues in contact with THR 700 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681H ILE 3.2 11.4 - - - +
682H MET* 4.9 5.2 - - + -
683H GLY* 3.5 13.0 + - - -
698H ASN* 4.3 6.8 + - - -
699H ILE* 1.3 76.1 + - - +
701H ILE* 1.3 74.2 + - - +
702H ARG* 6.3 0.4 - - + +
907H ILE* 4.1 19.9 - - - +
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Residues in contact with ILE 701 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679H VAL* 4.4 2.9 - - + +
680H GLN* 2.9 21.1 - - - +
681H ILE* 3.0 43.0 + - + +
699H ILE* 3.8 13.2 - - + -
700H THR* 1.3 90.1 - - - +
702H ARG* 1.3 70.4 + - - +
703H ILE* 3.6 24.7 - - + -
722H LEU* 3.5 29.2 - - + -
900H ILE* 4.8 15.3 - - + -
907H ILE* 3.9 16.6 - - + -
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Residues in contact with ARG 702 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677H CYS* 3.3 34.9 - - - +
678H CYS 4.2 2.7 - - - -
679H VAL 4.0 4.3 - - - -
680H GLN* 2.5 30.3 + - - +
682H MET* 5.8 4.6 - - - +
700H THR* 6.3 0.6 - - + +
701H ILE* 1.3 79.0 + - - +
703H ILE* 1.3 70.4 + - - +
704H PRO* 4.2 5.8 - - + +
898H TRP* 3.2 37.3 + - + +
900H ILE* 4.9 1.7 - - - +
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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