Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 4N36
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 251 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209B PHE* 3.9 24.0 - + + +
210B SER 4.0 11.6 + - - -
245B THR 5.1 1.7 + - - -
246B ALA* 3.5 41.0 + - + -
249B LEU* 3.3 27.7 - - + +
250B ILE* 1.3 73.9 - - - +
252B TRP* 1.3 63.8 + - - +
253B ILE* 3.4 1.4 + - - +
297B ASN* 3.1 4.0 - - - +
298B ILE* 2.9 37.8 + - + +
316B LEU* 3.2 40.2 - - + +
317B PHE 3.5 10.3 - - - -
318B ILE* 3.6 33.7 - - + -
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Residues in contact with TRP 252 (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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214B LYS 3.1 28.3 + - - -
215B THR 4.0 1.1 - - - -
216B TRP* 3.3 32.3 - + + +
219B ALA* 4.6 3.6 - - + -
230B LEU* 4.1 6.6 - - + +
251B TYR* 1.3 71.4 - - - +
253B ILE* 1.3 61.6 + - - +
295B CYS* 3.6 26.0 - - + -
296B GLY 3.3 24.5 - - - -
297B ASN* 3.7 18.1 - - + +
309B ALA* 3.8 17.7 - - + -
310B PRO 3.3 25.6 - - - -
311B CYS* 4.0 6.7 - - - -
313B ILE 3.2 21.1 + - - -
315B PHE* 3.6 33.1 - + + +
316B LEU 2.7 10.1 + - - -
317B PHE* 3.5 11.1 - - + +
318B ILE 3.1 24.6 + - - -
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Residues in contact with ILE 253 (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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216B TRP* 2.8 24.8 + - - -
230B LEU* 3.7 9.2 - - - +
231B THR* 3.6 27.6 - - + +
233B VAL* 4.1 7.6 - - + -
251B TYR 3.4 8.7 + - - +
252B TRP* 1.3 78.6 - - - +
254B GLY* 1.3 59.8 + - - +
255B LEU* 3.0 28.7 + - + -
266B TRP* 4.1 8.1 - - + -
296B GLY 3.1 17.5 + - - +
297B ASN* 4.3 2.0 - - - -
298B ILE* 3.8 22.2 - - + -
306B TRP* 3.6 34.1 - - + +
318B ILE* 4.3 4.9 - - + -
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Residues in contact with GLY 254 (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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216B TRP* 4.1 4.2 - - - -
230B LEU* 3.5 24.2 - - - +
231B THR 2.8 22.2 + - - -
253B ILE* 1.3 69.3 - - - +
255B LEU* 1.3 61.7 + - - +
256B THR* 3.4 0.9 + - - +
265B SER 3.3 4.7 - - - +
266B TRP* 3.4 8.6 - - - -
267B VAL* 2.9 33.7 + - - +
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Residues in contact with LEU 255 (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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216B TRP* 3.5 6.8 + - - -
253B ILE* 3.0 21.9 + - + -
254B GLY* 1.3 76.0 - - - +
256B THR* 1.3 62.9 + - - +
264B TRP* 3.8 13.2 - - + -
265B SER 3.6 4.0 - - - +
266B TRP* 3.4 29.2 - - + -
272B PHE* 3.6 25.4 - - + -
281B TRP* 4.0 12.3 - - + -
295B CYS* 3.3 3.1 - - - -
296B GLY* 3.0 44.7 + - - +
306B TRP* 3.7 29.6 - - + -
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Residues in contact with THR 256 (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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216B TRP* 3.7 22.7 - - + -
254B GLY 4.2 5.2 - - - +
255B LEU* 1.3 76.8 - - - +
257B LYS* 1.3 64.4 + - - +
258B ALA* 5.9 0.2 - - + -
264B TRP* 3.6 8.6 - - - -
265B SER* 2.8 45.2 + - - +
267B VAL* 4.6 9.6 - - + +
294B HIS 3.3 14.6 + - - -
295B CYS* 3.9 0.7 - - - -
217D TYR* 2.6 32.5 + - - +
221D GLN* 3.4 4.2 + - - -
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Residues in contact with LYS 257 (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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256B THR* 1.3 82.4 + - - +
258B ALA* 1.3 62.5 + - - +
259B GLY 5.7 0.2 - - - +
262B GLY* 3.6 31.4 - - - +
263B ASP 3.5 4.7 - - - +
264B TRP* 3.7 25.4 - - + +
288B ASP* 3.3 23.2 + - - +
293B GLU 3.0 19.8 + - - -
294B HIS* 2.9 43.5 + - + +
308B ASP* 5.4 0.4 - - - -
221D GLN* 3.1 32.4 + - - +
224D VAL* 4.3 6.3 - - + +
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Residues in contact with ALA 258 (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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256B THR* 5.9 0.2 - - + -
257B LYS* 1.3 77.5 - - - +
259B GLY* 1.3 69.8 + - - +
261B GLU* 5.8 0.2 - - - +
262B GLY 4.0 0.2 + - - -
263B ASP* 3.0 28.5 + - - +
265B SER* 3.6 23.1 - - - +
224D VAL* 3.8 6.5 - - - -
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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