Contacts of the strand formed by residues 381 - 385 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64L LEU* 4.3 9.9 - - + -
238L MET* 5.8 5.8 - - - -
239L PHE* 6.1 5.4 - + - -
379L GLY 3.5 0.6 - - - -
380L LEU* 1.3 92.0 - - + +
382L LEU* 1.3 60.7 + - - +
383L GLU* 3.4 27.8 - - + +
404L GLN* 3.4 26.9 - - + -
405L VAL 3.1 20.6 - - - +
406L PHE* 3.6 29.2 - + + -
407L LEU* 4.3 1.6 - - - +
485L TYR* 3.7 24.5 - + - -
487L PHE* 6.4 1.1 - + - -
602L 1CA 2.5 30.5 + - - +
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Residues in contact with LEU 382 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97L VAL* 5.1 1.6 - - + -
100L LEU* 6.0 0.2 - - + -
381L PHE* 1.3 76.5 - - - +
383L GLU* 1.3 60.6 + - - +
384L ARG* 5.1 1.8 - - - +
403L VAL 4.7 0.2 - - - -
404L GLN* 3.4 4.3 - - - -
405L VAL* 2.8 48.2 + - + +
407L LEU* 4.1 21.0 - - + +
441L VAL* 3.8 21.3 - - + +
444L GLY* 3.6 28.5 - - - +
445L PHE* 3.8 25.6 - - + -
601L HEM 3.4 38.6 - - + -
602L 1CA 3.7 4.5 - - - +
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Residues in contact with GLU 383 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU* 5.7 1.8 - - - -
109L CYS 4.5 1.8 - - - +
110L ARG* 4.7 15.6 + - - +
111L MET* 3.3 34.1 + - - +
381L PHE* 3.4 18.3 - - + +
382L LEU* 1.3 76.3 - - - +
384L ARG* 1.3 86.2 + - - +
402L LEU* 3.2 34.7 - - + +
403L VAL 3.6 4.9 - - - +
404L GLN* 3.2 26.2 - - + +
445L PHE* 6.4 0.2 - - - -
601L HEM 5.0 0.8 + - - -
602L 1CA 4.4 3.6 + - - +
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Residues in contact with ARG 384 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU* 4.6 21.3 - - + +
104L ASP* 3.1 31.0 + - - +
108L PRO* 4.1 8.7 - - + +
109L CYS 3.4 22.7 + - - +
110L ARG* 4.1 5.7 - - - +
382L LEU* 5.1 0.6 - - - +
383L GLU* 1.3 94.2 + - - +
385L VAL* 1.3 67.8 + - - +
386L VAL* 3.5 5.4 + - + +
401L THR 3.6 0.2 - - - +
402L LEU* 4.1 1.6 - - - -
403L VAL* 2.9 40.8 + - - +
445L PHE* 3.5 40.0 + - - -
448L ARG* 3.8 17.1 - - - +
601L HEM 2.4 43.6 + - - -
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Residues in contact with VAL 385 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109L CYS* 3.0 37.2 + - + +
110L ARG* 4.4 2.7 - - - +
111L MET* 3.7 49.8 - - + +
384L ARG* 1.3 72.3 - - - +
386L VAL* 1.3 64.0 + - - +
387L SER* 3.7 2.8 + - - -
400L GLY* 3.5 29.2 - - - +
401L THR 3.7 3.4 - - - -
402L LEU* 4.1 11.0 - - + +
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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