Contacts of the strand formed by residues 261 - 275 (chain B) in PDB entry 1VQM
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 GLN 261 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28080 U 2.7 41.8 + - - +
28090 G 3.8 27.1 + - - +
19B SER* 4.2 14.9 + - - +
21B SER 5.4 1.6 - - - +
23B THR 4.6 0.7 - - - +
24B PRO* 3.4 14.1 - - + +
25B ARG* 2.8 52.1 + - - +
27B ASN* 5.9 0.2 - - - +
203B ALA* 5.2 1.3 - - + +
204B GLY 3.6 8.5 - - - +
205B VAL* 4.2 6.5 - - + +
260B HIS* 1.3 73.3 - - - +
262B ARG* 1.3 86.5 + - - +
263B THR* 4.1 5.0 + - - +
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Residues in contact with ARG 262 (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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27150 G 2.9 38.4 + - - +
27160 G 3.2 21.5 + - - -
28070 U 5.6 0.2 - - - -
28080 U 3.8 9.9 + - - -
13B PHE* 3.3 51.9 + - - +
16B ARG* 4.5 8.5 - - - +
202B VAL 3.9 1.0 - - - +
203B ALA* 3.2 3.6 - - - +
204B GLY 2.9 34.8 + - - +
206B THR* 3.5 24.5 - - + -
260B HIS* 3.6 26.5 + - - +
261B GLN* 1.3 94.1 + - - +
263B THR* 1.3 63.8 + - - +
264B GLU* 3.9 3.6 - - + +
302B PRO* 4.2 11.1 - - + +
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Residues in contact with THR 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28070 U 3.5 28.5 + - - +
28080 U 2.8 23.9 + - - -
26B PHE* 4.4 10.9 - - + -
201B ASP* 4.4 6.7 - - + -
202B VAL 3.5 7.4 - - - +
203B ALA* 3.8 11.4 - - - +
261B GLN* 4.1 2.9 + - - -
262B ARG* 1.3 74.5 - - - +
264B GLU* 1.3 60.1 + - - +
265B LEU* 3.5 27.0 - - + +
312B ARG* 4.1 23.0 + - - +
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Residues in contact with GLU 264 (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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27150 G 2.7 32.4 + - - +
27160 G 3.6 23.0 + - - +
27650 C 3.3 2.8 - - - +
27660 A 4.1 12.6 - - - +
201B ASP* 3.4 1.9 - - - -
202B VAL* 2.7 42.7 + - + +
262B ARG* 3.9 3.9 - - + +
263B THR* 1.3 72.3 - - - +
265B LEU* 1.3 62.8 + - - +
267B LYS* 2.8 45.2 + - + +
300B SER* 4.1 4.6 + - - -
302B PRO* 3.8 18.9 - - + +
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Residues in contact with LEU 265 (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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27660 A 2.7 34.3 + - - +
27670 C 4.5 11.4 - - - -
28060 C 3.9 12.1 - - - +
28070 U 4.4 10.1 - - - -
201B ASP* 3.3 18.6 - - - +
263B THR* 3.5 33.4 - - + +
264B GLU* 1.3 79.3 - - - +
266B ASN* 1.3 76.3 + - - +
267B LYS* 3.5 2.8 + - - +
312B ARG* 4.7 2.2 - - - +
316B ARG* 3.3 44.2 - - + +
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Residues in contact with ASN 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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27660 A 3.7 23.1 - - - +
27670 C 2.8 30.3 + - - +
199B TYR* 3.7 24.8 - - + -
200B ALA 3.7 2.7 - - - -
201B ASP* 3.0 10.0 + - - +
265B LEU* 1.3 78.3 - - - +
267B LYS* 1.3 61.3 + - - +
268B ARG 3.6 2.8 + - - -
314B ALA* 3.6 10.9 - - - +
316B ARG* 3.1 28.8 + - - +
317B PRO* 3.4 13.5 - - - +
318B ASN* 3.5 15.0 - - - +
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Residues in contact with LYS 267 (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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27650 C 2.7 29.0 + - - +
27660 A 3.3 10.9 + - - +
199B TYR* 4.0 0.4 - - - -
200B ALA* 2.6 44.2 + - - +
202B VAL* 3.9 21.5 - - + -
264B GLU* 2.8 53.3 + - - +
265B LEU 4.2 3.1 - - - +
266B ASN* 1.3 71.6 - - - +
268B ARG* 1.3 62.7 + - - +
269B LEU* 3.5 2.5 + - + +
297B VAL* 3.6 18.6 - - + -
298B LYS 3.9 12.1 - - - +
300B SER* 3.1 25.3 + - - +
301B VAL* 5.3 0.7 - - - +
302B PRO* 5.6 0.2 - - - -
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Residues in contact with ARG 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LEU* 4.5 5.9 - - - +
56B ASP* 3.6 16.6 + - - +
197B GLY 3.8 19.0 + - - +
198B GLU 3.6 4.0 - - - +
199B TYR* 3.3 31.7 + - + -
266B ASN 3.6 4.8 + - - -
267B LYS* 1.3 71.9 - - - +
269B LEU* 1.3 67.6 + - - +
270B ILE* 3.4 17.4 + - - +
297B VAL* 3.8 0.5 - - - -
298B LYS* 2.8 56.9 + - + +
322B ARG* 2.9 56.8 + - - +
325B PRO* 3.0 29.9 - - - +
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Residues in contact with LEU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190B MET* 5.7 2.0 - - - -
194B PHE* 3.5 45.1 - - + -
195B ARG 4.5 5.6 - - - +
196B ALA* 4.6 4.9 - - - -
197B GLY* 2.6 37.5 + - - +
198B GLU* 2.9 21.0 + - + +
200B ALA* 4.2 15.9 - - + -
267B LYS 4.4 1.8 - - - +
268B ARG* 1.3 72.1 - - - +
270B ILE* 1.3 60.6 + - - +
271B ASP 3.5 1.8 - - - +
272B ILE* 4.6 7.6 - - + -
295B THR* 3.9 24.7 - - + -
296B LEU 3.8 3.1 - - - +
297B VAL* 3.9 17.3 - - + -
311B PHE* 4.2 12.3 - - + -
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B VAL* 4.4 9.0 - - + -
53B LEU* 3.5 33.9 - - + -
69B VAL* 4.9 4.3 - - + -
71B VAL* 4.0 16.2 - - + -
196B ALA* 3.9 3.4 - - - +
268B ARG* 4.1 26.5 - - - +
269B LEU* 1.3 74.3 - - - +
271B ASP* 1.3 63.9 + - + +
296B LEU* 2.7 25.8 + - + +
298B LYS* 4.1 23.6 - - + -
325B PRO* 3.9 21.3 - - + +
327B VAL* 3.9 25.2 - - + +
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B ALA* 4.0 10.8 - - - +
269B LEU 3.5 2.2 - - - -
270B ILE* 1.3 86.6 - - + +
272B ILE* 1.3 75.1 + - - +
273B GLY* 4.8 0.7 - - - -
294B TYR* 3.3 27.4 + - - +
295B THR* 3.4 4.2 - - - +
296B LEU* 2.8 47.5 + - + +
327B VAL* 4.8 10.3 - - + -
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Residues in contact with ILE 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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76B THR* 5.1 0.2 - - - +
190B MET* 3.7 37.2 - - + +
191B ASN* 3.9 25.3 - - - +
194B PHE* 3.5 34.1 - - + +
195B ARG* 4.1 1.3 - - - -
196B ALA* 3.8 25.9 - - + +
269B LEU* 4.6 6.5 - - + -
271B ASP* 1.3 86.4 + - - +
273B GLY* 1.3 62.5 + - - +
294B TYR 3.5 9.9 - - - +
295B THR* 4.5 9.4 - - + +
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Residues in contact with GLY 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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271B ASP* 4.8 1.6 - - - -
272B ILE* 1.3 78.3 - - - +
274B GLU* 1.3 63.5 + - - +
293B PRO* 3.4 4.5 - - - +
294B TYR* 2.9 47.3 + - - +
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Residues in contact with GLU 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 GLY* 1.3 75.9 - - - +
275B GLY* 1.3 64.8 + - - +
277B GLU* 3.8 12.3 - - - +
292B GLY* 3.1 21.7 - - - +
293B PRO* 3.9 21.7 - - + +
294B TYR* 3.5 7.0 - - - -
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Residues in contact with GLY 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 GLU* 1.3 81.2 - - - +
276B ASP* 1.3 57.8 + - - -
277B GLU* 3.7 5.6 - - - -
290B VAL* 3.8 5.2 - - - +
291B ASP* 2.8 35.8 + - - -
292B GLY 2.9 12.7 + - - +
294B TYR* 4.1 3.5 - - - -
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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