Contacts of the strand formed by residues 382 - 388 (chain A) in PDB entry 3CWL
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 PRO 382 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A THR 4.7 2.0 - - - +
30A LEU* 3.8 38.4 - - + +
31A ALA* 4.0 14.8 - - + +
34A ALA* 4.0 7.0 - - + -
54A PRO* 3.3 23.8 - - + +
55A VAL* 3.3 11.9 - - + +
373A LEU* 4.1 24.0 - - + -
374A MET 3.6 6.5 - - - +
375A ILE* 3.8 7.2 - - + -
380A LYS 3.8 4.7 - - - +
381A SER* 1.3 82.9 - - - +
383A LEU* 1.3 63.3 + - - +
384A PHE 3.3 2.9 - - - +
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Residues in contact with LEU 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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53A SER* 2.6 29.2 + - - +
54A PRO* 3.4 0.4 - - - +
55A VAL* 4.0 16.2 - - + -
103A LEU* 3.6 35.7 - - + -
110A LEU* 4.3 16.2 - - + -
112A LEU* 4.4 16.6 - - + -
190A PHE* 5.9 1.8 - - + -
248A ALA* 4.2 21.5 - - + -
374A MET* 2.8 14.1 + - + +
376A GLU* 3.9 26.7 - - + +
381A SER* 3.1 6.4 + - - -
382A PRO* 1.3 71.9 - - - +
384A PHE* 1.3 80.2 + - + +
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Residues in contact with PHE 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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51A PHE* 3.4 36.3 - + + -
52A PHE 3.4 6.5 - - - -
53A SER* 3.8 11.0 - - - -
54A PRO* 3.8 4.7 - - - -
112A LEU* 3.7 22.2 - - + -
188A ILE* 3.6 31.4 - - + -
190A PHE* 3.4 45.8 - + + -
337A VAL 5.4 0.2 - - - -
373A LEU* 3.3 9.9 - - - +
374A MET* 3.1 53.7 + - + +
382A PRO 3.3 1.6 - - - -
383A LEU* 1.3 96.2 - - + +
385A MET* 1.3 63.9 + - - +
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Residues in contact with MET 385 (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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34A ALA* 4.1 11.2 - - - +
35A PHE* 4.1 19.3 - - + -
38A TYR* 3.6 45.1 - - + -
51A PHE* 3.5 3.1 - - - -
52A PHE* 3.1 50.0 + - + +
54A PRO* 4.0 5.1 - - + +
267A LEU* 4.0 26.7 - - + -
371A VAL* 4.0 10.8 - - + -
372A PHE* 3.4 16.6 - - - +
373A LEU* 3.9 19.7 - - + -
384A PHE* 1.3 75.6 - - - +
386A GLY* 1.3 62.1 + - - +
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Residues in contact with GLY 386 (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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38A TYR* 4.1 4.9 - - - -
50A ILE* 2.9 18.8 - - - -
371A VAL* 3.4 10.7 - - - +
372A PHE* 2.9 48.1 + - - -
385A MET* 1.3 77.1 - - - +
387A LYS* 1.3 59.9 + - - -
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Residues in contact with LYS 387 (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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38A TYR* 3.4 22.2 + - + +
42A ALA* 4.4 9.9 - - - +
46A ASN* 4.5 21.4 + - - +
48A THR 4.5 2.9 - - - -
49A ASN* 3.4 8.0 - - - +
50A ILE* 2.8 47.2 + - + +
260A LEU* 4.2 26.3 - - + +
264A GLU* 2.8 25.7 + - - +
293A ILE* 4.9 0.5 - - - +
369A PRO* 5.2 0.4 - - + -
370A PHE 3.3 15.9 - - - +
371A VAL* 4.3 1.6 - - + -
372A PHE* 3.9 1.0 - - - -
386A GLY* 1.3 74.1 - - - +
388A VAL* 1.3 68.8 + - - +
389A VAL* 3.8 26.7 - - + -
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Residues in contact with VAL 388 (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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49A ASN* 3.8 4.9 - - - +
208A PHE* 3.9 8.3 - - + -
291A LEU* 4.1 17.7 - - + -
293A ILE* 4.5 11.4 - - + -
369A PRO* 3.0 27.4 - - - +
370A PHE* 3.0 42.6 + - + +
372A PHE* 4.2 13.5 - - + -
387A LYS* 1.3 75.2 - - - +
389A VAL* 1.3 62.1 + - - +
390A ASN 4.3 0.7 - - - -
391A PRO* 3.7 40.6 - - + -
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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