Contacts of the strand formed by residues 381 - 385 (chain H) in PDB entry 4DVQ
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 381 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64H LEU* 4.3 10.3 - - + -
238H MET* 4.6 14.1 - - + -
239H PHE* 5.6 4.0 - + - -
379H GLY 3.3 1.8 - - - -
380H LEU* 1.3 84.4 - - + +
382H LEU* 1.3 71.2 + - - +
383H GLU* 3.7 17.2 - - + +
404H GLN* 3.2 28.3 - - + -
405H VAL 3.0 15.5 - - - +
406H PHE* 3.6 32.5 - + + -
407H LEU* 4.8 0.9 - - - -
485H TYR* 3.7 32.5 - + - -
487H PHE* 6.3 0.7 - + - -
602H 1CA 2.8 27.4 + - - +
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Residues in contact with LEU 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H VAL* 5.1 1.3 - - + -
381H PHE* 1.3 74.2 - - - +
383H GLU* 1.3 63.1 + - - +
403H VAL 4.5 0.4 - - - -
404H GLN* 3.3 8.5 - - - +
405H VAL* 2.9 45.1 + - + -
407H LEU* 4.0 24.0 - - + -
441H VAL* 3.8 24.7 - - + +
444H GLY* 3.6 22.7 - - - +
445H PHE* 4.0 24.0 - - + -
601H HEM 3.5 39.7 - - + +
602H 1CA 3.8 4.9 - - - +
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Residues in contact with GLU 383 (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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100H LEU* 6.1 0.2 - - - -
109H CYS 4.0 3.1 - - - +
110H ARG* 3.8 17.4 + - + +
111H MET* 2.9 44.9 + - - +
381H PHE* 3.7 27.2 - - + +
382H LEU* 1.3 79.9 - - - +
384H ARG* 1.3 92.5 + - - +
402H LEU* 3.6 23.6 - - + +
403H VAL 3.6 4.9 - - - +
404H GLN* 3.8 8.1 - - + +
601H HEM 5.0 0.6 + - - -
602H 1CA 4.8 2.5 + - - +
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Residues in contact with ARG 384 (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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100H LEU* 4.3 22.9 - - + +
104H ASP* 3.0 26.5 + - - +
108H PRO* 4.1 12.9 - - - +
109H CYS 3.2 16.2 - - - +
110H ARG* 4.1 4.4 - - - +
382H LEU* 5.2 0.2 - - - +
383H GLU* 1.3 104.9 + - - +
385H VAL* 1.3 66.8 + - - +
386H VAL* 3.5 3.8 + - + +
402H LEU* 3.7 3.3 - - - -
403H VAL* 2.9 33.8 + - - +
445H PHE* 3.3 49.5 + - + -
448H ARG* 3.7 14.7 - - - +
601H HEM 2.8 42.4 + - - -
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Residues in contact with VAL 385 (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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109H CYS* 2.9 34.8 + - + +
110H ARG* 4.3 2.0 - - - +
111H MET* 4.0 35.7 - - + +
384H ARG* 1.3 73.2 - - - +
386H VAL* 1.3 65.9 + - - +
387H SER* 3.5 4.0 + - - -
400H GLY* 3.8 26.9 - - - +
401H THR 3.5 4.0 - - - +
402H LEU* 4.5 15.3 - - + -
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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