Contacts of the strand formed by residues 731 - 738 (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 GLN 731 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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405H SER* 5.6 0.4 + - - -
687H THR* 2.6 57.5 + - + +
688H TRP 4.4 9.7 + - - +
690H PRO* 5.4 9.0 - - + -
729H GLU 3.8 2.2 + - - -
730H MET* 1.3 66.5 - - - +
732H LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 732 (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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685H TYR 3.0 15.7 - - - +
686H PHE* 3.4 25.1 - - + -
730H MET 2.9 7.3 + - - +
731H GLN* 1.3 72.3 - - - +
733H VAL* 1.3 62.8 + - - +
734H SER* 4.1 9.4 - - - +
735H GLY 3.6 25.7 + - - +
736H ALA* 5.8 0.2 - - - +
737H VAL* 4.6 13.7 - - + +
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Residues in contact with VAL 733 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685H TYR* 2.8 21.8 + - + -
686H PHE 4.6 1.6 - - - -
687H THR* 3.7 31.0 - - + -
690H PRO* 6.2 0.4 - - + -
694H PRO* 4.3 15.7 - - + -
731H GLN 3.5 0.6 + - - -
732H LYS* 1.3 75.2 + - - +
734H SER* 1.3 63.8 + - - +
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Residues in contact with SER 734 (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 4.6 0.3 + - - -
684H GLY* 3.7 0.9 - - - -
685H TYR* 2.6 60.5 + - - +
686H PHE* 4.8 0.9 - - - -
732H LYS* 3.3 11.8 - - - +
733H VAL* 1.3 83.7 - - - +
735H GLY* 1.3 66.3 + - - +
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Residues in contact with GLY 735 (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* 4.6 2.0 - - - -
682H MET 3.5 15.9 - - - -
683H GLY 3.6 7.0 - - - -
684H GLY* 4.1 5.8 - - - -
686H PHE* 6.0 0.4 - - - -
732H LYS* 3.6 25.7 + - - +
734H SER* 1.3 84.5 + - - +
736H ALA* 1.3 59.9 + - - -
737H VAL* 4.9 1.3 - - - -
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Residues in contact with ALA 736 (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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680H GLN 3.6 0.5 - - - +
681H ILE* 3.2 24.5 - - - +
682H MET* 3.2 20.5 + - + +
732H LYS* 5.8 0.2 - - - +
735H GLY* 1.3 73.4 - - - +
737H VAL* 1.3 61.8 - - - +
738H PHE* 4.0 27.2 + - + -
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Residues in contact with VAL 737 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679H VAL* 4.7 0.7 - - + -
680H GLN 3.4 10.8 - - - +
681H ILE* 3.6 25.8 - - + -
686H PHE* 4.3 17.9 - - + -
725H ALA 5.9 1.3 - - - +
726H ALA* 5.0 7.2 - - - +
732H LYS* 4.6 16.5 - - + +
735H GLY 4.9 0.2 - - - -
736H ALA* 1.3 79.4 - - - +
738H PHE* 1.3 62.9 + - - +
739H TRP* 3.2 43.3 + - + +
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Residues in contact with PHE 738 (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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678H CYS 5.5 0.4 - - - -
679H VAL* 3.2 17.9 - - - -
680H GLN* 3.3 38.3 + - + +
682H MET* 4.9 19.3 - - + -
736H ALA* 4.0 28.5 - - + -
737H VAL* 1.3 76.4 - - - +
739H TRP* 1.3 70.4 + - - +
740H SER 5.2 2.5 - - - +
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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
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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