Contacts of the helix formed by residues 676 - 681 (chain A) in PDB entry 4D9T
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 HIS 676 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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651A THR* 3.4 26.5 - - + -
654A ASP* 3.0 26.6 + - + -
655A LEU* 3.5 35.8 + - + -
658A LYS* 4.8 5.2 - - - -
668A LEU* 4.6 9.9 - - + -
672A LEU 3.3 8.5 + - - +
673A VAL 3.2 14.4 + - - +
675A ARG* 1.3 80.0 - - - +
677A PRO* 1.3 72.2 - - + +
678A TRP* 2.9 31.5 + - - +
679A ILE* 3.0 10.2 + - + +
680A VAL* 2.8 29.0 + - - +
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Residues in contact with PRO 677 (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 THR* 4.0 9.1 - - + +
675A ARG 3.6 5.1 - - - +
676A HIS* 1.3 103.5 - - + +
678A TRP* 1.3 59.1 + - - +
680A VAL* 3.6 3.8 - - + +
681A HIS* 2.7 53.5 + - + +
685A LEU* 5.5 0.5 - - - +
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Residues in contact with TRP 678 (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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513A GLU* 3.5 31.7 + - - -
516A ALA* 3.5 15.3 - - + -
517A SER* 3.0 53.1 + - - -
520A LEU* 4.1 9.6 - - + -
608A LEU* 3.6 24.7 - - + -
612A LEU* 4.1 9.9 - - + -
649A SER* 4.3 0.9 - - - -
651A THR* 3.3 19.5 - - + +
652A ALA* 3.1 42.4 - - + +
655A LEU* 3.4 22.2 - - + -
676A HIS* 2.9 17.3 + - + +
677A PRO* 1.3 77.6 - - - +
679A ILE* 1.3 64.3 + - + +
682A TRP 3.8 3.3 + - - -
685A LEU* 3.5 32.2 - - + +
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Residues in contact with ILE 679 (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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517A SER* 3.8 11.7 + - - +
520A LEU* 4.1 18.8 - - + -
521A PHE* 3.8 53.6 - - + +
524A THR* 5.5 0.2 - - - +
655A LEU* 4.6 4.9 - - + -
673A VAL* 3.4 28.7 - - + +
674A LEU* 3.9 21.8 - - + +
676A HIS* 3.0 9.4 + - + +
678A TRP* 1.3 89.7 - - + +
680A VAL* 1.3 63.6 + - - +
682A TRP* 3.7 17.2 + - - +
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Residues in contact with VAL 680 (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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674A LEU 3.4 23.1 - - - +
675A ARG* 4.0 13.5 - - + +
676A HIS 2.8 15.2 + - - +
677A PRO* 4.1 5.8 - - + -
679A ILE* 1.3 78.0 - - + +
681A HIS* 1.3 82.7 + - + +
682A TRP* 3.2 20.1 + - - -
683A ASP* 4.7 0.7 - - - +
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Residues in contact with HIS 681 (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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677A PRO* 2.7 40.4 + - + +
678A TRP 4.3 0.7 - - - -
680A VAL* 1.3 89.7 + - + +
682A TRP* 1.3 54.2 + - - +
683A ASP* 2.9 10.9 + - - -
684A GLN* 2.6 66.1 + - + +
685A LEU* 3.7 5.2 + - - +
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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