Contacts of the strand formed by residues 287 - 295 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ILE* 3.8 21.5 - - + -
149C PRO* 3.9 23.5 + - + +
152C ALA* 3.1 32.6 - - + +
153C GLU* 4.4 9.9 + - - +
156C LYS* 4.4 6.6 + - - -
161C TYR* 4.3 2.9 + - - -
166C ILE* 6.2 0.2 - - + -
277C PHE* 3.5 27.3 - - + -
278C VAL 3.2 6.5 - - - +
279C LYS* 3.6 39.7 - - + +
280C SER 4.1 0.2 - - - +
285C CYS* 3.3 16.2 - - - +
286C THR* 1.3 96.2 - - - +
288C PHE* 1.3 66.4 + - - +
323C LEU* 4.8 1.0 - - - +
327C ILE* 3.6 26.5 - - + +
331C GLU* 4.1 8.0 + - - -
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Residues in contact with PHE 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 4.1 13.9 - - + -
198C GLY* 3.6 15.7 - - - -
206C ILE* 5.0 3.6 - - + -
276C SER 3.6 1.7 - - - +
277C PHE* 3.6 12.5 - - - -
278C VAL* 2.9 29.7 + - - +
280C SER* 3.7 20.9 + - - +
282C GLU* 4.9 1.6 - - + -
283C THR* 3.5 37.7 - - + +
285C CYS* 4.2 4.0 - - + -
287C TYR* 1.3 74.9 - - - +
289C SER* 1.3 87.9 + - - +
290C THR* 3.9 18.5 + - + -
305C ILE* 4.2 11.0 - - + -
316C ILE* 4.4 15.5 - - + -
319C ALA* 6.0 0.2 - - + -
320C ILE* 5.1 2.7 - - + -
323C LEU* 3.7 30.3 - - + -
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Residues in contact with SER 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C THR* 3.6 14.5 + - - +
196C VAL 3.8 10.9 + - - -
197C ILE* 3.1 12.8 - - - +
198C GLY 2.7 42.5 + - - -
199C GLY 5.6 0.4 - - - -
275C CYS 3.9 0.2 - - - -
276C SER* 3.2 35.7 + - - -
277C PHE* 3.6 7.9 - - - -
288C PHE* 1.3 73.8 - - - +
290C THR* 1.3 63.2 + - - +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197C ILE* 4.1 5.2 - - + -
275C CYS* 3.3 14.7 - - - -
276C SER 3.5 2.6 + - - -
280C SER* 4.8 0.2 + - - -
282C GLU* 4.2 5.5 - - + +
288C PHE* 3.9 13.5 + - + -
289C SER* 1.3 79.1 + - - +
291C PRO* 1.3 76.3 - - + +
292C LEU* 3.3 16.8 + - - +
302C ASN* 2.6 36.4 + - - -
304C GLY* 3.7 24.7 - - - +
305C ILE* 3.8 19.3 - - + -
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Residues in contact with PRO 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C PRO* 4.5 15.7 - - + -
197C ILE* 4.1 9.4 - - + -
208C LEU* 6.0 0.7 - - + -
211C GLN* 5.4 3.4 - - - +
273C VAL* 3.8 18.2 - - + -
274C GLU 3.9 2.0 - - - +
275C CYS* 3.9 26.5 - - - +
290C THR* 1.3 89.7 - - + +
292C LEU* 1.3 61.4 + - - +
302C ASN* 3.7 1.6 - - - +
303C LEU* 3.0 36.7 + - + +
304C GLY 3.5 15.3 - - - +
305C ILE 5.7 0.7 - - - +
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Residues in contact with LEU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C PHE* 4.2 6.1 - - + -
258C PHE* 5.8 0.2 - - + -
273C VAL* 3.2 8.7 - - - +
274C GLU 2.9 33.8 + - - +
276C SER* 3.8 18.6 - - - +
278C VAL* 3.7 36.6 - - + -
290C THR* 3.3 20.4 - - - +
291C PRO* 1.3 77.9 - - - +
293C LEU* 1.3 63.9 + - - +
294C LEU* 3.5 14.7 + - + +
299C ILE* 4.1 19.5 - - + -
301C LYS 3.7 3.8 - - - +
302C ASN* 3.7 32.1 - - + +
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Residues in contact with LEU 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C GLY* 3.9 15.0 - - - +
272C VAL 3.5 29.6 - - - +
273C VAL* 4.4 7.4 - - + -
292C LEU* 1.3 70.7 - - - +
294C LEU* 1.3 59.4 + - - +
299C ILE* 3.8 3.3 - - - +
300C GLU* 2.8 50.8 + - + -
301C LYS* 2.8 33.1 + - + +
303C LEU* 4.0 21.7 - - + +
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Residues in contact with LEU 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C PHE* 4.1 23.3 - - + -
258C PHE* 4.9 7.2 - - + -
261C SER* 4.3 7.2 - - - +
262C LEU* 4.2 20.4 - - + +
265C ALA* 3.6 21.0 - - + +
269C LYS 4.6 5.5 - - - +
270C GLU* 5.9 0.2 - - - -
271C GLY 5.5 0.3 + - - -
272C VAL* 2.9 35.8 + - + +
274C GLU* 4.2 22.4 - - + +
292C LEU* 3.9 25.1 - - + +
293C LEU* 1.3 87.5 - - - +
295C GLY* 1.3 60.0 + - - +
298C GLY 3.4 11.7 - - - +
299C ILE* 4.4 2.9 - - - -
300C GLU* 4.0 2.5 - - - +
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 5.5 0.7 - - - +
265C ALA* 3.5 23.5 - - - +
266C MET* 3.9 4.3 + - - +
269C LYS 5.6 1.1 - - - -
294C LEU* 1.3 74.7 - - - +
296C LYS* 1.3 64.6 + - - -
297C LYS 3.2 4.1 + - - -
298C GLY* 2.8 18.0 + - - +
300C GLU* 3.8 22.3 - - - +
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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