Contacts of the strand formed by residues 278 - 287 (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 ALA 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A VAL* 3.4 5.1 - - - +
10A ILE* 2.9 29.2 + - + +
276A PRO 3.3 1.2 - - - -
277A LEU* 1.3 81.4 - - - +
279A ARG* 1.3 64.8 + - - +
367A LEU* 3.5 26.0 - - + +
370A LEU* 5.4 1.1 - - + -
394A VAL* 4.2 9.0 - - + -
395A GLN 3.4 20.9 - - - +
396A ARG* 4.1 2.2 - - + +
397A GLU* 3.8 11.0 - - - +
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Residues in contact with ARG 279 (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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7A PRO* 4.1 20.3 - - + +
8A VAL 3.7 6.1 - - - +
9A VAL* 4.0 10.8 - - + -
278A ALA* 1.3 77.3 - - - +
280A ILE* 1.4 63.2 + - - +
281A VAL* 3.8 23.8 - - + +
394A VAL* 3.2 5.6 - - - +
395A GLN* 2.8 80.7 + - + +
396A ARG 5.9 0.2 + - - -
397A GLU* 3.5 29.6 + - + +
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Residues in contact with ILE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 4.1 13.5 - - - +
8A VAL* 2.8 26.2 + - + +
10A ILE* 3.8 31.9 - - + -
99A VAL* 4.2 2.0 - - + -
103A VAL* 3.5 39.7 - - + -
263A LEU* 3.7 19.7 - - + -
279A ARG* 1.4 72.0 + - - +
281A VAL* 1.3 64.5 + - - +
282A SER* 4.2 9.9 - - - +
283A TRP* 5.2 1.3 - - + -
392A MET* 4.0 31.2 - - + -
393A CYS 3.8 6.5 - - - +
394A VAL* 4.4 2.5 - - + -
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A ARG* 3.8 27.1 - - + +
280A ILE* 1.3 77.1 - - - +
282A SER* 1.3 58.8 + - - +
307A LYS 5.3 0.9 - - - +
308A ALA* 3.5 34.5 - - + +
310A TRP* 3.9 13.0 - - + +
393A CYS* 2.8 20.4 + - + +
395A GLN* 3.8 32.8 - - + +
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Residues in contact with SER 282 (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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280A ILE* 3.8 4.0 - - - +
281A VAL* 1.3 80.7 - - - +
283A TRP* 1.3 71.2 + - - +
304A ALA 2.7 28.2 + - - -
307A LYS* 3.8 20.4 - - - -
308A ALA* 3.7 7.3 - - - +
392A MET* 3.4 4.7 - - - +
393A CYS* 2.8 40.7 + - - +
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Residues in contact with TRP 283 (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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97A LYS* 4.0 10.1 - - - -
100A CYS* 3.4 44.0 + - + -
103A VAL* 4.3 26.3 - - + +
104A GLN* 3.5 34.9 - - + +
280A ILE* 5.2 2.0 - - + -
282A SER* 1.3 82.9 - - - +
284A SER* 1.3 72.8 + - - +
285A GLN* 3.6 42.4 - - + -
304A ALA* 4.3 5.2 - - - -
307A LYS* 2.7 39.0 + - - +
390A ILE* 4.8 2.9 - - + -
391A ALA 3.1 14.8 - - - +
392A MET* 4.1 10.8 - - + +
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Residues in contact with SER 284 (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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283A TRP* 1.3 83.5 - - - +
285A GLN* 1.3 60.7 + - - +
286A VAL* 4.8 2.9 - - - -
300A ALA* 2.7 39.5 + - - +
303A GLN* 4.1 13.0 - - - -
304A ALA* 3.7 11.5 - - - +
307A LYS* 4.2 9.0 - - - +
390A ILE* 3.3 9.0 - - - +
391A ALA* 2.9 27.6 + - - +
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Residues in contact with GLN 285 (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* 3.8 22.9 - - + +
97A LYS* 2.7 36.9 + - - +
283A TRP* 3.6 18.6 - - + -
284A SER* 1.3 75.1 - - - +
286A VAL* 1.3 66.7 + - - +
303A GLN* 4.8 2.3 - - - +
389A GLY 3.3 8.1 - - - +
390A ILE* 4.7 4.3 - - + -
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Residues in contact with VAL 286 (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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284A SER* 4.8 1.1 - - - -
285A GLN* 1.3 82.2 - - - +
287A GLY* 1.3 63.1 + - - +
288A VAL* 4.8 0.9 - - + -
296A GLY 3.5 24.5 - - - +
299A PRO* 3.9 13.0 - - + -
300A ALA* 3.8 20.6 - - + +
303A GLN* 3.5 36.6 - - - +
388A MET* 3.2 13.2 - - - +
389A GLY 2.9 38.3 + - - +
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Residues in contact with GLY 287 (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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286A VAL* 1.3 76.5 - - - +
288A VAL* 1.3 69.4 + - - +
299A PRO* 5.4 0.7 - - - +
387A GLY 3.3 7.9 - - - -
388A MET* 4.3 4.3 - - - -
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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