Contacts of the strand formed by residues 381 - 385 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I LEU* 4.4 8.1 - - + -
238I MET* 4.5 13.9 - - + -
239I PHE* 5.6 2.5 - + - -
379I GLY 3.4 1.0 - - - -
380I LEU* 1.3 86.2 - - + +
382I LEU* 1.3 57.4 + - - +
383I GLU* 3.3 40.2 + - + +
404I GLN* 3.8 18.2 - - + -
405I VAL 3.0 17.5 - - - +
406I PHE* 3.4 37.9 - + + -
407I LEU* 4.7 1.1 - - - -
485I TYR* 3.8 27.8 - + - -
487I PHE* 6.3 2.2 - + - -
602I 1CA 2.6 31.7 + - - +
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Residues in contact with LEU 382 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I VAL* 4.6 1.3 - - + -
100I LEU* 6.3 0.9 - - + -
381I PHE* 1.3 75.7 - - - +
383I GLU* 1.3 60.8 + - - +
384I ARG* 5.3 1.1 - - - +
403I VAL 3.6 0.7 - - - +
404I GLN* 3.2 8.3 - - - +
405I VAL* 2.9 43.1 + - + +
407I LEU* 3.9 17.5 - - + -
441I VAL* 3.8 34.3 - - + +
444I GLY* 3.6 22.2 - - - +
445I PHE* 3.9 25.4 - - + -
601I HEM 3.5 40.4 - - + +
602I 1CA 3.8 4.9 - - - +
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Residues in contact with GLU 383 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109I CYS 4.1 3.8 - - - +
110I ARG* 4.1 22.3 + - + +
111I MET* 3.3 37.9 + - - +
238I MET* 5.9 1.4 - - - +
381I PHE* 3.3 36.2 + - + +
382I LEU* 1.3 72.2 - - - +
384I ARG* 1.3 82.9 + - - +
402I LEU* 4.2 10.8 - - + +
403I VAL 3.5 2.2 - - - -
404I GLN* 3.5 22.4 - - + +
602I 1CA 4.6 2.7 + - - +
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Residues in contact with ARG 384 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I LEU* 4.0 25.1 - - + +
104I ASP* 3.3 31.0 + - - +
108I PRO* 3.7 13.9 - - - +
109I CYS 3.3 13.0 - - - +
110I ARG* 4.3 1.8 - - - +
382I LEU* 5.3 0.4 - - - +
383I GLU* 1.3 91.8 + - - +
385I VAL* 1.3 60.5 + - - +
386I VAL* 3.3 8.2 + - - +
402I LEU* 3.7 3.5 - - - +
403I VAL* 2.9 34.7 + - - +
445I PHE* 3.0 55.1 + - + -
448I ARG* 3.5 22.7 - - - +
601I HEM 3.1 30.7 + - - -
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Residues in contact with VAL 385 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I CYS* 2.7 40.5 + - + +
110I ARG* 4.5 2.0 - - - +
111I MET* 4.3 27.1 - - + +
384I ARG* 1.3 68.2 - - - +
386I VAL* 1.3 65.4 + - - +
387I SER* 3.3 4.5 + - - -
400I GLY* 4.1 27.1 - - - +
401I THR 3.3 6.3 - - - +
402I LEU* 3.4 26.0 - - + +
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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