Contacts of the strand formed by residues 377 - 384 (chain A) in PDB entry 1WL4
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 ARG 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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310A TRP* 3.6 47.8 - - + +
314A ASP* 3.5 35.7 + - - +
315A VAL* 4.3 1.6 - - - -
316A ASP* 2.8 37.8 + - - +
317A ILE 3.3 6.6 + - - -
370A LEU* 3.9 4.0 - - - +
376A SER* 1.3 93.2 + - - +
378A GLY* 1.3 59.5 + - - +
394A VAL 3.5 3.1 - - - -
395A GLN* 3.5 30.5 + - - +
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Residues in contact with GLY 378 (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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310A TRP* 4.0 2.3 - - - -
315A VAL* 4.2 0.7 - - - -
317A ILE 3.1 10.8 - - - -
366A LEU* 4.0 9.9 - - - -
370A LEU* 4.1 17.0 - - - +
377A ARG* 1.3 76.0 - - - +
379A VAL* 1.3 65.6 + - - +
393A CYS* 3.4 4.3 - - - -
394A VAL* 2.9 34.9 + - - +
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Residues in contact with VAL 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 4.0 23.3 - - + -
305A VAL* 4.1 7.2 - - + -
310A TRP* 4.6 0.4 - - + -
315A VAL* 3.7 27.1 - - + -
317A ILE 3.0 6.1 + - - -
318A PHE* 3.3 24.7 - - + -
319A GLU 2.8 26.3 + - - +
366A LEU* 3.6 7.1 - - - +
378A GLY* 1.3 79.4 - - - +
380A ALA* 1.3 74.5 + - - +
381A ALA* 4.5 0.4 - - + -
391A ALA* 4.7 4.7 - - + -
392A MET 3.2 6.5 - - - +
393A CYS* 3.9 20.4 - - - -
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Residues in contact with ALA 380 (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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96A LEU* 3.8 14.4 - - + +
319A GLU* 3.2 6.7 - - + -
362A ILE* 4.1 19.3 - - + -
363A LEU* 4.5 19.3 - - + +
366A LEU* 3.8 14.6 - - + +
379A VAL* 1.3 73.3 - - - +
381A ALA* 1.3 62.0 + - - +
391A ALA* 3.1 4.2 - - - +
392A MET* 2.8 35.1 + - + +
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Residues in contact with ALA 381 (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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297A PRO* 4.1 11.4 - - + -
301A ILE* 3.6 36.8 - - + -
319A GLU 2.8 9.2 + - - +
320A ILE* 3.3 6.2 - - + +
321A ASN 3.0 25.5 + - - -
362A ILE* 3.5 2.6 - - - +
379A VAL* 4.5 0.9 - - + -
380A ALA* 1.3 77.6 - - - +
382A LEU* 1.3 67.8 + - - +
390A ILE 3.1 11.9 - - - +
391A ALA* 3.8 2.5 - - + -
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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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92A CSO 3.4 24.9 - - + +
93A GLY* 4.8 0.7 - - - -
96A LEU* 3.8 23.1 - - + -
297A PRO* 3.5 9.7 - - - +
321A ASN* 3.6 33.7 - - + +
358A SER* 4.0 4.7 - - - -
359A GLY* 3.6 32.3 - - - +
362A ILE* 3.7 12.6 - - + -
381A ALA* 1.3 81.1 - - - +
383A CYS* 1.3 67.1 + - - +
384A ILE* 4.1 0.2 - - - +
389A GLY* 3.4 4.5 - - - -
390A ILE* 2.9 41.7 + - + +
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Residues in contact with CYS 383 (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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92A CSO 3.5 19.6 - - - +
293A MET* 3.4 45.8 - - - +
294A GLY* 3.5 19.5 - - - +
297A PRO* 3.5 10.5 - - + +
321A ASN* 5.3 7.8 + - - +
323A ALA* 3.9 22.7 - - - -
327A VAL* 4.7 4.5 - - - -
382A LEU* 1.3 76.8 - - - +
384A ILE* 1.3 65.4 + - - +
388A MET 3.7 5.2 - - - -
1001A COA 4.7 2.7 - - - -
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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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90A MET* 3.2 39.7 - - + +
91A ILE* 4.0 7.2 - - + -
92A CSO 4.0 3.1 - - - +
93A GLY* 3.7 26.5 - - - +
293A MET* 3.4 10.6 - - - +
382A LEU 4.1 4.3 - - - +
383A CYS* 1.3 83.2 - - - +
385A GLY* 1.3 77.8 + - - +
387A GLY 3.1 3.6 + - - -
388A MET* 2.9 59.1 + - + +
389A GLY 4.1 7.4 - - - -
390A ILE* 3.9 17.0 - - + -
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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