Contacts of the strand formed by residues 379 - 384 (chain A) in PDB entry 4G84
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 CYS 379 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 4.3 6.3 - - + -
139A LEU* 4.1 4.3 - - - -
178A ILE 3.5 6.7 - - - +
179A ALA* 3.4 22.4 - - - -
362A ARG* 3.3 8.4 - - - +
363A TYR* 2.8 65.2 + - + +
364A ASP* 3.2 5.1 + - - -
367A VAL* 3.9 20.0 - - - -
377A VAL 3.5 10.0 + - - -
378A PRO* 1.3 81.7 - - - +
380A VAL* 1.3 60.4 + - - +
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Residues in contact with VAL 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ASP* 3.5 5.4 - - - +
178A ILE* 2.8 36.8 + - + +
187A PRO* 4.0 20.4 - - + -
188A ASP* 3.8 27.1 - - + +
191A CYS* 4.1 6.6 - - - -
334A VAL* 4.5 0.9 - - + -
336A TYR* 3.4 17.3 - - + +
361A GLY* 3.3 21.1 - - - +
362A ARG* 3.4 28.0 - - - +
363A TYR* 4.2 1.6 - - - -
379A CYS* 1.3 75.2 - - - +
381A GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE 3.1 13.7 - - - -
177A ASP* 3.4 9.7 + - - -
191A CYS* 3.9 7.9 - - - -
336A TYR* 2.9 17.3 + - - -
360A GLY* 3.4 0.2 - - - -
361A GLY 3.1 23.3 + - - -
380A VAL* 1.3 77.4 - - - +
382A LEU* 1.3 61.3 + - - -
1001A IMD 3.3 9.4 - - - -
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Residues in contact with LEU 382 (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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84A PHE* 4.5 8.1 - - + -
174A CYS 4.7 0.2 - - - +
175A ASP* 3.2 5.7 - - - -
176A PHE* 2.8 57.0 + - + +
191A CYS* 3.4 39.7 - - + +
194A ILE* 4.0 15.7 - - + -
195A MET* 4.1 17.9 - - + +
336A TYR* 4.3 2.2 - - + -
359A ALA 3.3 10.1 - - - +
381A GLY* 1.3 73.9 - - - +
383A SER* 1.3 59.3 + - - +
384A ILE* 3.5 36.1 - - + -
1001A IMD 3.3 10.2 + - - -
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Residues in contact with SER 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLN* 3.8 18.5 + - - -
174A CYS 3.4 5.6 - - - -
175A ASP* 2.6 26.1 + - - -
358A ALA* 3.1 5.9 - - - +
359A ALA* 2.7 38.0 + - - -
382A LEU* 1.3 71.7 - - - +
384A ILE* 1.3 65.5 + - - +
385A GLY 3.6 0.3 + - - -
1001A IMD 3.6 12.7 - - - -
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Residues in contact with ILE 384 (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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80A ILE* 4.4 7.9 - - + -
84A PHE* 4.5 1.1 - - + -
172A TYR 4.9 0.2 - - - +
173A GLN* 4.8 1.9 - - - -
174A CYS* 2.8 49.1 + - + +
195A MET* 4.6 8.7 - - + +
198A ILE* 4.2 33.9 - - + -
199A LEU* 5.2 4.3 - - + -
357A VAL 3.9 3.8 - - - +
358A ALA* 4.1 14.6 - - + -
382A LEU* 3.5 28.3 - - + -
383A SER* 1.3 72.6 - - - +
385A GLY* 1.3 62.0 + - - +
386A VAL* 2.9 17.6 + - + +
389A ILE* 3.6 27.4 - - + -
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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