Contacts of the strand formed by residues 287 - 295 (chain A) in PDB entry 4WLU
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 TYR 287 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A ILE* 3.8 18.8 - - + -
149A PRO* 3.8 30.3 + - + +
152A ALA* 3.2 29.0 - - + +
153A GLU* 4.6 9.0 + - - -
156A LYS* 4.7 6.4 + - - -
161A TYR* 4.0 10.0 + - - -
277A PHE* 3.5 28.5 - - + -
278A VAL 3.2 6.1 - - - +
279A LYS* 3.6 39.5 - - + +
280A SER* 4.2 0.4 - - - +
285A CYS* 3.4 15.1 - - - +
286A THR* 1.3 95.4 - - - +
288A PHE* 1.3 66.6 + - - +
323A LEU* 4.7 1.6 - - - +
327A ILE* 3.6 19.3 - - + +
331A GLU* 4.2 7.9 + - + +
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Residues in contact with PHE 288 (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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197A ILE* 4.2 8.5 - - + -
198A GLY* 3.6 22.2 - - - -
206A ILE* 4.7 3.4 - - + -
276A SER 3.7 1.6 - - - +
277A PHE* 3.6 8.1 - - - -
278A VAL* 3.0 29.1 + - - +
280A SER* 3.6 20.1 - - - +
282A GLU* 4.7 6.1 - - + -
283A THR* 3.6 36.8 - - + +
285A CYS* 4.1 3.8 - - + +
287A TYR* 1.3 74.9 - - - +
289A SER* 1.3 90.1 + - - +
290A THR* 3.9 11.3 + - + -
305A ILE* 4.0 17.5 - - + -
316A ILE* 4.2 19.1 - - + -
319A ALA* 5.7 0.4 - - + -
320A ILE* 5.0 2.9 - - + -
323A LEU* 3.7 30.1 - - + -
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Residues in contact with SER 289 (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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170A THR* 3.5 15.4 + - - +
196A VAL 3.9 9.8 + - - -
197A ILE* 3.1 13.1 - - - +
198A GLY 2.7 45.2 + - - -
199A GLY* 4.6 0.7 - - - -
275A CYS 4.0 0.3 - - - -
276A SER 3.3 32.4 + - - -
277A PHE* 3.8 8.5 - - - -
288A PHE* 1.3 74.8 - - - +
290A THR* 1.3 63.7 + - - +
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Residues in contact with THR 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ILE* 4.0 4.7 - - + -
275A CYS* 3.4 15.4 - - - -
276A SER 3.5 3.4 + - - -
280A SER* 4.9 0.5 + - - -
282A GLU* 4.0 8.5 - - + -
288A PHE* 3.9 11.9 + - + -
289A SER* 1.3 79.0 + - - +
291A PRO* 1.3 72.9 - - + +
292A LEU* 3.3 16.5 - - - +
302A ASN* 2.6 37.1 + - - -
304A GLY 3.7 22.4 - - - +
305A ILE* 3.9 19.7 - - + -
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Residues in contact with PRO 291 (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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195A PRO* 4.2 17.0 - - + -
197A ILE* 4.1 13.0 - - + -
208A LEU* 5.8 0.4 - - + -
211A GLN* 5.3 4.3 - - - +
273A VAL* 3.9 18.4 - - + -
274A GLU 3.8 5.6 - - - +
275A CYS* 3.8 19.9 - - - -
290A THR* 1.3 89.4 - - - +
292A LEU* 1.3 61.1 + - - +
302A ASN* 3.7 1.4 - - - +
303A LEU* 3.0 36.2 + - + +
304A GLY 3.5 15.0 - - - +
305A ILE* 5.4 0.7 - - - +
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Residues in contact with LEU 292 (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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167A PHE* 4.2 5.4 - - + -
258A PHE* 5.8 0.2 - - + -
273A VAL* 3.2 8.1 - - - +
274A GLU 2.8 34.5 + - - +
276A SER* 3.8 21.3 - - - +
278A VAL* 3.8 35.2 - - + -
290A THR* 3.3 17.7 - - - +
291A PRO* 1.3 72.3 - - - +
293A LEU* 1.3 61.7 + - - +
294A LEU* 3.4 13.9 + - + +
299A ILE* 4.0 20.9 - - + -
301A LYS 3.6 4.3 - - - +
302A ASN* 3.6 38.1 - - + +
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Residues in contact with LEU 293 (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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271A GLY* 3.9 28.3 - - - +
272A VAL 3.5 17.7 - - - +
273A VAL* 4.3 8.3 - - + -
292A LEU* 1.3 70.4 - - - +
294A LEU* 1.3 58.4 + - - +
299A ILE* 3.7 2.8 - - - -
300A GLU* 2.8 51.5 + - + +
301A LYS* 2.8 35.7 + - + +
303A LEU* 4.0 16.5 - - + +
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Residues in contact with LEU 294 (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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167A PHE* 4.3 15.0 - - + -
258A PHE* 5.0 3.4 - - + -
261A SER* 4.2 9.9 - - - -
262A LEU* 3.5 31.2 - - + +
265A ALA* 3.6 19.2 - - + +
269A LYS 4.7 4.7 - - - +
270A GLU* 5.9 0.2 - - - -
271A GLY 5.5 0.3 + - - -
272A VAL* 2.9 35.7 + - + +
274A GLU* 4.2 22.2 - - + +
292A LEU* 3.9 28.0 - - + +
293A LEU* 1.3 85.5 - - - +
295A GLY* 1.3 58.7 + - - +
298A GLY* 3.3 11.2 - - - +
299A ILE* 4.4 2.7 - - - -
300A GLU* 3.9 2.1 - - - +
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Residues in contact with GLY 295 (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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136A MET* 5.1 0.2 - - - +
262A LEU 4.9 0.3 - - - +
265A ALA* 3.5 23.8 - - - +
266A MET* 3.8 3.3 + - - +
269A LYS 5.6 1.1 - - - -
294A LEU* 1.3 73.5 - - - +
296A LYS* 1.3 65.2 + - - -
297A LYS 3.2 4.1 + - - -
298A GLY* 2.6 21.1 + - - +
300A GLU* 3.8 20.8 - - - +
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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