Contacts of the strand formed by residues 331 - 341 (chain B) in PDB entry 4F4W
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 ILE 331 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B MET* 3.1 23.4 - - + +
255B ASN* 3.2 6.9 - - - -
256B SER 2.9 36.2 + - - +
262B ILE* 4.2 6.5 - - + -
289B ALA* 4.0 21.8 - - + -
290B VAL 3.8 4.0 - - - +
291B THR* 4.2 4.9 - - + +
320B LEU* 3.9 21.3 - - + -
323B ILE* 4.4 8.7 - - + -
324B LEU* 3.7 25.4 - - + -
329B ARG 4.4 8.1 - - - +
330B LYS* 1.3 76.9 - - - +
332B ARG* 1.3 57.8 - - - +
333B ARG 3.1 28.3 - - - +
334B ILE* 4.5 5.8 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ARG* 3.3 42.8 + - - +
40B SER* 4.6 4.0 - - - -
251B THR* 3.8 4.9 - - + +
252B MET* 3.0 32.6 + - - +
255B ASN* 3.3 23.1 + - - +
290B VAL* 2.7 15.7 + - - +
291B THR 4.1 10.8 - - - +
292B GLU* 4.2 8.2 + - - +
294B LEU* 4.0 24.6 - - - +
330B LYS 4.0 1.4 + - - -
331B ILE* 1.3 73.3 - - - +
333B ARG* 1.3 67.1 + - + +
4F C 3.7 20.4 + - - -
5F G 3.0 40.9 + - - -
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Residues in contact with ARG 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ILE* 4.1 11.0 - - + -
250B VAL 3.1 12.6 - - - +
251B THR* 3.2 24.1 + - - +
252B MET* 5.0 0.4 - - - -
289B ALA* 3.4 1.4 - - - -
290B VAL* 2.9 65.6 + - + +
294B LEU* 4.6 12.5 - - - +
296B ILE* 6.1 1.4 - - - +
331B ILE* 3.1 12.5 - - - +
332B ARG* 1.3 84.4 - - + +
334B ILE* 1.3 59.5 + - - +
4F C 4.2 11.9 + - - +
5F G 2.7 66.4 + - - +
6F G 3.7 15.0 + - - -
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Residues in contact with ILE 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B ILE* 3.7 4.0 - - - -
250B VAL* 3.0 30.0 + - + +
252B MET* 4.2 8.5 - - + -
262B ILE* 3.7 24.0 - - + -
265B TYR* 3.5 31.2 - - + -
266B LEU* 4.1 21.3 - - + +
269B ALA* 4.8 1.7 - - - +
287B VAL* 3.9 18.8 - - + -
288B VAL 3.5 15.7 - - - +
289B ALA* 4.1 13.0 - - + -
320B LEU* 4.1 18.6 - - + -
331B ILE* 4.5 6.3 - - + -
333B ARG* 1.3 74.9 - - - +
335B GLY* 1.3 60.0 + - - +
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Residues in contact with GLY 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ARG 3.1 13.5 - - - -
249B ILE* 3.8 7.4 - - - +
266B LEU* 3.9 2.3 - - - +
269B ALA* 4.5 6.5 - - - -
287B VAL* 3.5 7.4 - - - +
288B VAL* 2.9 33.8 + - - -
334B ILE* 1.3 79.1 - - - +
336B VAL* 1.3 70.3 + - - +
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Residues in contact with VAL 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLY* 3.1 3.0 - - - -
248B ARG 2.9 34.5 + - - +
249B ILE* 4.9 0.8 - - - +
266B LEU* 3.2 31.4 - - + -
269B ALA* 3.9 19.5 - - + +
270B ILE* 3.8 15.0 - - + -
273B SER* 3.7 12.8 - - - +
285B ILE* 4.8 4.7 - - + -
286B HIS 3.3 6.7 - - - +
287B VAL* 4.2 12.8 - - + -
288B VAL* 4.7 1.0 - - - +
316B SER* 4.7 1.1 - - - -
335B GLY* 1.3 71.7 - - - +
337B ARG* 1.3 67.5 + - - +
338B PHE* 3.6 26.7 - - + -
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Residues in contact with ARG 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B SER* 3.2 27.7 + - - -
246B ILE 3.7 5.8 - - - +
247B GLY* 4.6 5.6 - - - -
248B ARG 5.4 0.2 - - - +
284B ALA 4.5 0.2 - - - -
285B ILE* 3.5 3.8 - - - +
286B HIS* 2.9 46.5 + - + +
288B VAL* 4.1 20.9 - - + -
336B VAL* 1.3 79.2 - - - +
338B PHE* 1.3 64.0 + - - +
339B SER* 4.4 0.6 + - - -
9E T 4.6 7.7 + - - +
10E C 4.3 4.2 - - - +
8F C 3.5 39.7 + - - +
9F G 2.9 48.3 + - - -
10F A 5.2 1.2 - - - +
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Residues in contact with PHE 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B SER* 3.0 6.5 - - - -
246B ILE 2.8 40.7 + - - +
270B ILE* 4.3 9.9 - - + -
273B SER* 3.8 21.1 - - - -
274B TYR* 3.5 29.4 - + - -
277B LEU* 4.3 15.3 - - + -
282B PRO* 3.7 29.2 - - + -
284B ALA 3.3 10.8 - - - -
285B ILE* 3.7 32.5 - - + -
307B ILE* 4.9 2.5 - - + -
312B ALA* 3.9 11.2 - - + -
336B VAL* 3.6 24.2 - - + -
337B ARG* 1.3 74.5 - - - +
339B SER* 1.3 62.7 + - - +
341B PHE* 3.6 3.5 - - - -
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Residues in contact with SER 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LYS 3.5 17.5 - - - -
245B SER* 4.1 8.1 - - - -
282B PRO* 3.6 2.8 - - - +
283B LYS 3.2 3.8 + - - -
284B ALA* 3.1 36.5 + - - +
286B HIS* 4.8 7.8 + - - -
337B ARG* 5.3 1.1 + - - -
338B PHE* 1.3 75.4 - - - +
340B LYS* 1.3 80.4 + - - +
341B PHE* 3.5 7.6 - - - -
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Residues in contact with LYS 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B LYS 4.1 5.1 + - - -
283B LYS* 2.9 46.9 + - + +
284B ALA* 3.9 10.8 - - + -
286B HIS* 6.1 1.8 - - - -
302B THR* 2.8 36.6 + - + +
339B SER* 1.3 81.3 - - - +
341B PHE* 1.3 62.5 + - - +
6E T 3.1 41.1 + - - +
7E G 3.8 10.5 + - - -
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Residues in contact with PHE 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243B ARG* 3.5 26.2 - - + -
244B LYS* 3.8 11.4 - - - -
245B SER* 3.8 14.8 - - - -
246B ILE* 3.9 6.3 - - + -
277B LEU* 3.4 30.1 - - + -
280B ARG* 3.9 31.0 - - + -
281B ILE 3.3 5.4 - - - +
282B PRO* 3.9 17.0 - - + -
283B LYS* 4.1 4.0 + - - -
338B PHE 3.6 26.9 - - - -
339B SER* 3.8 6.5 - - - -
340B LYS* 1.3 77.5 - - - +
342B ILE* 1.3 69.4 + - - +
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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