Contacts of the strand formed by residues 265 - 275 (chain B) in PDB entry 4NSW
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 GLY 265 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B GLU* 4.7 4.3 - - - -
262B GLY* 2.8 32.1 + - - -
264B GLY* 1.3 79.9 - - - +
266B LEU* 1.3 69.3 + - - -
267B VAL* 3.6 3.8 - - - +
292B SER* 5.6 2.0 - - - -
293B ASN* 6.0 3.8 - - - -
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Residues in contact with LEU 266 (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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259B LEU* 4.7 20.9 - - + -
260B ARG 3.3 10.5 - - - +
261B GLU* 3.3 38.4 - - + +
262B GLY 4.4 0.4 - - - +
265B GLY* 1.3 74.4 - - - -
267B VAL* 1.3 60.2 + - - +
290B ILE* 3.7 20.5 - - - +
291B GLN* 4.2 4.7 - - - -
292B SER 4.7 1.7 + - - -
293B ASN* 5.8 1.3 + - - +
354B ALA 5.9 0.4 - - - +
357B SER* 4.6 28.7 - - - +
358B SER* 4.9 17.8 + - - +
360B ALA 6.1 0.4 - - - +
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Residues in contact with VAL 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B SER 3.7 0.9 - - - +
259B LEU* 3.9 0.9 - - - -
260B ARG* 2.6 60.4 + - - +
262B GLY* 3.7 17.7 - - - -
263B PRO* 5.2 1.3 - - + +
264B GLY 6.0 0.9 - - - -
265B GLY 3.6 11.4 - - - +
266B LEU* 1.3 78.8 - - - +
268B MET* 1.3 71.4 + - - +
269B GLU* 5.5 4.3 - - + -
289B THR* 4.6 4.0 - - + -
290B ILE* 3.2 12.1 - - - +
291B GLN* 3.7 40.4 - - + +
292B SER 5.7 0.4 - - - +
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Residues in contact with MET 268 (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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257B PRO* 3.6 27.6 - - + +
258B SER 3.4 15.5 - - - +
259B LEU* 3.6 30.1 - - + -
260B ARG* 5.7 2.0 - - - +
267B VAL* 1.3 78.0 - - - +
269B GLU* 1.3 65.3 + - - +
288B PHE 4.6 0.2 - - - -
289B THR* 3.4 2.8 - - - +
290B ILE* 2.8 44.5 + - + +
350B LEU* 4.6 3.8 - - + +
351B TRP* 3.1 58.8 - - + +
354B ALA* 3.6 17.3 - - + -
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Residues in contact with GLU 269 (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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9A GLU* 4.8 1.6 - - - +
12A LYS* 2.8 32.4 + - - +
257B PRO* 3.1 22.9 - - - +
260B ARG* 6.1 4.9 - - - +
267B VAL* 5.5 4.7 - - + -
268B MET* 1.3 78.0 - - - +
270B GLY* 1.3 58.6 + - - +
287B TRP* 3.3 34.7 + - + +
288B PHE 3.1 12.6 - - - +
289B THR* 3.8 10.9 + - + +
351B TRP* 4.3 2.9 - - - -
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Residues in contact with GLY 270 (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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257B PRO* 4.1 9.4 - - - -
269B GLU* 1.3 75.5 - - - +
271B HIS* 1.3 63.0 - - - -
287B TRP* 3.5 21.2 - - - -
288B PHE* 2.8 33.6 + - - +
351B TRP* 3.8 12.5 - - - -
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Residues in contact with HIS 271 (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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12A LYS 4.2 6.5 - - - -
13A ASP* 2.9 34.4 + - + -
15A PRO* 4.7 5.6 - - + -
163A ARG* 6.1 1.1 - - - -
255B PRO* 6.0 2.9 - - + -
257B PRO* 5.4 0.8 - - - +
270B GLY* 1.3 72.6 - - - -
272B LEU* 1.3 72.0 + - - +
285B ARG* 3.1 47.2 + - + +
286B ARG 3.2 19.1 + - - +
287B TRP* 3.4 39.0 - + + -
299B LYS 5.7 2.5 - - - -
343B ASP* 4.3 7.8 - - - +
347B LEU* 5.8 2.1 - - - +
351B TRP* 4.1 5.2 + - - +
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Residues in contact with LEU 272 (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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270B GLY 3.8 1.0 + - - -
271B HIS* 1.3 82.1 - - - +
273B PHE* 1.3 72.1 + - - +
285B ARG* 3.4 5.0 - - - +
286B ARG 2.9 29.5 + - - +
288B PHE* 3.7 23.8 - - + -
295B LEU* 6.0 0.4 - - + -
329B PHE* 4.0 16.2 - - + -
340B LEU* 4.4 11.9 - - + -
341B GLN 3.4 19.3 - - - +
342B ALA* 3.8 13.9 - - + +
343B ASP* 5.5 0.4 - - - -
347B LEU* 6.5 0.2 - - + -
351B TRP* 3.4 59.0 - - + +
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Residues in contact with PHE 273 (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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138A LEU 3.6 20.6 - - - -
139A THR* 3.7 28.9 - - + -
142A ALA* 3.7 19.3 - - + -
272B LEU* 1.3 78.4 - - - +
274B LYS* 1.3 59.9 + - - +
283B TRP* 3.9 8.3 - - + -
284B SER* 3.4 25.4 - - - -
285B ARG* 3.4 35.2 - - + -
325B ARG* 4.3 11.2 - - - -
340B LEU* 3.4 5.0 - - - +
341B GLN* 3.0 52.4 + - + +
342B ALA 5.5 0.2 - - - -
343B ASP* 3.4 25.1 - - - -
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Residues in contact with LYS 274 (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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273B PHE* 1.3 75.7 - - - +
275B ARG* 1.3 80.1 + - - +
276B ALA* 4.2 5.6 - - - +
277B SER* 5.6 3.4 + - - +
282B THR 3.6 1.4 - - - +
283B TRP* 3.1 8.6 - - - -
284B SER* 2.8 45.9 + - - +
286B ARG* 4.4 10.3 - - + -
288B PHE* 3.7 20.6 - - + -
297B TYR* 3.5 38.3 - - + +
308B VAL* 4.3 18.8 - - - +
338B CYS* 4.7 8.9 - - - +
339B LEU 3.6 8.5 + - - -
340B LEU* 4.2 3.5 - - + +
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Residues in contact with ARG 275 (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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274B LYS* 1.3 90.5 + - - +
276B ALA* 1.3 73.1 + - - +
277B SER* 3.8 2.3 + - - -
281B LYS* 3.4 59.1 - - - +
282B THR 3.6 1.3 - - - -
283B TRP* 3.6 35.0 - - + +
323B SER* 5.9 3.8 - - - -
324B GLU* 5.8 2.4 + - - -
339B LEU* 3.1 57.2 + - + +
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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