Contacts of the strand formed by residues 331 - 341 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A MET* 3.3 19.7 - - + +
255A ASN* 3.1 8.6 - - - -
256A SER 3.0 33.6 + - - +
262A ILE* 4.2 6.5 - - + -
289A ALA* 4.0 20.6 - - + -
290A VAL 3.8 4.5 - - - +
291A THR* 4.2 6.5 - - + +
320A LEU* 3.9 21.5 - - + -
323A ILE* 4.4 9.0 - - + -
324A LEU* 3.7 26.5 - - + -
329A ARG 4.4 7.2 - - - +
330A LYS* 1.3 76.1 - - - +
332A ARG* 1.3 57.5 + - - +
333A ARG 3.1 27.6 - - - +
334A ILE* 4.5 6.5 - - + -
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Residues in contact with ARG 332 (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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36A ARG* 3.3 41.8 + - - +
40A SER* 4.7 4.0 - - - -
251A THR* 3.9 4.8 - - + +
252A MET* 3.0 33.0 + - - +
255A ASN* 3.4 24.1 + - - +
290A VAL 2.7 15.2 + - - +
291A THR 3.9 10.8 - - - +
292A GLU 4.4 6.7 + - - +
294A LEU* 3.7 24.7 - - - +
330A LYS 4.0 1.4 + - - -
331A ILE* 1.3 74.1 - - - +
333A ARG* 1.3 65.9 + - + +
4T C 3.8 21.0 + - - -
5T G 3.0 39.2 + - - -
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Residues in contact with ARG 333 (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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249A ILE* 4.1 11.6 - - + +
250A VAL 3.2 10.8 - - - +
251A THR* 3.2 23.4 + - - +
252A MET* 5.0 0.2 - - - -
289A ALA* 3.4 0.9 - - - -
290A VAL* 2.9 65.4 + - + +
294A LEU* 4.3 11.3 - - - +
296A ILE* 6.0 1.6 - - - +
331A ILE* 3.1 12.1 - - - +
332A ARG* 1.3 85.0 - - + +
334A ILE* 1.3 62.8 + - - +
4T C 4.2 11.5 + - - +
5T G 2.8 66.1 + - - +
6T G 3.7 16.3 + - - -
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Residues in contact with ILE 334 (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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249A ILE* 3.6 4.4 - - - -
250A VAL* 3.0 31.0 + - + +
252A MET* 4.2 6.7 - - + -
262A ILE* 3.8 22.2 - - + -
265A TYR* 3.6 31.4 - - + -
266A LEU* 4.1 22.0 - - + +
269A ALA* 4.8 1.4 - - - +
287A VAL* 3.9 19.3 - - + -
288A VAL 3.5 15.0 - - - +
289A ALA* 4.2 13.2 - - + -
320A LEU* 4.1 19.7 - - + -
331A ILE* 4.5 6.5 - - + -
333A ARG* 1.3 73.9 - - - +
335A GLY* 1.3 59.0 + - - +
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Residues in contact with GLY 335 (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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248A ARG 3.1 14.1 - - - -
249A ILE* 3.7 8.0 - - - +
266A LEU* 3.9 2.1 - - - +
269A ALA* 4.4 7.2 - - - -
287A VAL* 3.4 6.8 - - - +
288A VAL* 2.9 32.4 + - - -
334A ILE* 1.3 79.5 - - - +
336A VAL* 1.3 70.4 + - - +
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Residues in contact with VAL 336 (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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247A GLY* 3.1 3.2 - - - -
248A ARG 2.9 29.0 + - - +
249A ILE* 4.9 0.6 - - - +
266A LEU* 3.4 21.5 - - + -
269A ALA* 3.9 24.5 - - + -
270A ILE* 3.9 14.4 - - + +
273A SER* 3.8 18.2 - - - +
285A ILE* 4.6 6.5 - - + -
286A HIS 3.2 6.5 - - - +
287A VAL* 4.0 15.5 - - + +
288A VAL* 4.6 0.8 - - - +
316A SER* 4.5 2.0 - - - -
335A GLY* 1.3 80.3 - - - +
337A ARG* 1.3 67.1 + - - +
338A PHE* 3.9 17.3 - - + -
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Residues in contact with ARG 337 (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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245A SER* 3.2 27.7 + - - -
246A ILE 3.8 5.4 - - - +
247A GLY* 4.6 5.8 - - - -
284A ALA 3.9 0.5 - - - +
285A ILE* 3.5 3.6 - - - +
286A HIS* 2.8 47.0 + - + +
288A VAL* 4.1 22.2 - - + -
336A VAL* 1.3 80.5 - - - +
338A PHE* 1.3 64.2 + - - +
339A SER* 4.3 1.0 + - - -
9P T 4.7 7.5 + - - +
10P C 4.4 3.8 - - - +
8T C 3.5 38.8 + - - +
9T G 2.9 48.7 + - - -
10T A 5.2 0.8 - - - +
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Residues in contact with PHE 338 (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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245A SER* 3.1 6.6 - - - -
246A ILE 2.9 43.4 + - - +
270A ILE* 4.2 10.1 - - + -
273A SER* 3.7 27.8 - - - -
274A TYR* 3.5 30.1 - + - -
277A LEU* 4.3 12.1 - - + -
282A PRO* 3.7 28.9 - - + -
284A ALA 3.4 9.9 - - - -
285A ILE* 3.7 32.5 - - + -
307A ILE* 4.9 2.7 - - + -
312A ALA* 3.9 12.3 - - + -
336A VAL* 3.9 15.5 - - + -
337A ARG* 1.3 75.8 - - - +
339A SER* 1.3 61.7 + - - +
341A PHE* 3.7 6.0 - - + -
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Residues in contact with SER 339 (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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244A LYS* 3.4 22.2 - - - -
245A SER* 4.0 7.6 - - - -
282A PRO* 3.6 2.4 - - - +
283A LYS 3.2 4.0 + - - -
284A ALA* 3.1 37.0 + - - +
286A HIS* 4.8 8.1 + - - -
337A ARG* 5.2 0.4 + - - -
338A PHE* 1.3 77.1 - - - +
340A LYS* 1.3 79.4 + - - +
341A PHE* 3.5 7.8 - - - -
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Residues in contact with LYS 340 (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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244A LYS* 4.0 11.2 + - - +
283A LYS* 2.9 48.1 + - + +
284A ALA* 4.0 8.5 - - + -
286A HIS* 6.2 1.3 - - - -
302A THR* 2.9 35.3 + - + +
339A SER* 1.3 86.4 - - - +
341A PHE* 1.3 61.8 + - - +
6P T 3.0 42.9 + - - +
7P G 3.8 10.6 + - - -
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Residues in contact with PHE 341 (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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243A ARG* 3.5 26.9 - - + -
244A LYS* 3.7 11.9 - - - -
245A SER* 3.7 26.0 - - - -
246A ILE* 4.0 7.2 - - + -
277A LEU* 3.4 28.9 - - + -
280A ARG* 3.9 31.9 - - + -
281A ILE 3.3 4.9 - - - +
282A PRO* 3.9 15.5 - - + -
283A LYS* 4.0 4.1 + - - -
338A PHE 3.7 16.2 - - - -
339A SER* 3.8 6.7 - - - -
340A LYS* 1.3 78.4 - - - +
342A ILE* 1.3 67.4 + - - +
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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