Contacts of the helix formed by residues 295 - 313 (chain B) in PDB entry 2VGL
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 GLU 295 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B ASN* 5.1 0.2 - - - +
294B GLY* 1.3 72.9 - - - -
296B PRO* 1.3 75.7 - - - +
297B GLU* 4.3 1.0 - - - +
298B VAL* 2.7 28.5 - - + +
299B GLN* 2.9 12.9 + - - +
60M ARG* 3.5 25.1 + - - -
83M TYR* 3.2 49.4 - - + +
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Residues in contact with PRO 296 (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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294B GLY 4.2 2.7 - - - +
295B GLU* 1.3 98.0 - - + +
297B GLU* 1.3 75.0 + - - +
299B GLN* 3.3 20.5 - - + +
300B TYR* 3.1 16.6 + - - +
331B PRO* 4.0 21.5 - - + -
333B TYR* 3.8 15.4 - - - +
334B VAL* 3.3 10.4 - - + +
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Residues in contact with GLU 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 4.3 2.1 - - - +
296B PRO* 1.3 88.2 - - - +
298B VAL* 1.3 57.3 + - - +
300B TYR* 3.0 25.8 + - - +
301B VAL* 3.2 8.8 + - - +
333B TYR* 3.9 10.5 + - - -
44M ARG* 5.5 4.7 + - - -
46M PRO* 4.0 22.1 - - + +
57M HIS 4.2 8.0 - - - +
58M VAL* 4.1 17.2 - - + +
59M LYS 5.1 1.7 + - - -
60M ARG* 4.8 4.3 + - - -
79M PHE* 3.4 37.7 - - + -
83M TYR* 2.5 36.4 + - - +
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASN* 5.8 0.2 - - - +
253B SER* 2.8 43.7 - - - +
257B LEU* 6.2 0.7 - - + -
291B LEU* 5.1 2.0 - - - +
294B GLY* 4.2 4.3 - - - -
295B GLU* 2.7 46.9 - - + +
297B GLU* 1.3 77.3 - - - +
299B GLN* 1.3 65.1 - - - +
300B TYR 3.0 1.8 + - - -
301B VAL* 3.1 9.1 + - + +
302B ALA* 2.8 23.8 + - + +
76M ALA* 4.9 12.8 - - + +
79M PHE* 4.9 6.1 - - + -
80M GLU* 3.7 11.7 - - + +
83M TYR* 4.1 11.0 - - + -
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B LEU 4.1 13.7 - - - +
292B LEU* 3.5 33.1 + - - +
293B SER 5.5 0.2 - - - -
294B GLY 3.7 15.8 + - - +
295B GLU 2.9 20.9 + - - +
296B PRO* 3.3 22.6 - - + +
298B VAL* 1.3 76.4 - - - +
300B TYR* 1.3 55.8 + - - +
302B ALA* 3.8 6.7 - - - +
303B LEU* 2.9 37.8 + - + +
327B LYS* 6.3 0.6 - - - +
330B ASP* 4.5 15.7 + - - +
331B PRO* 5.8 0.6 - - - +
334B VAL* 3.7 24.4 - - + +
338B LYS* 4.7 5.9 - - - -
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Residues in contact with TYR 300 (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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296B PRO 3.1 7.3 + - - +
297B GLU 3.0 10.9 + - - +
298B VAL 3.0 0.8 + - - -
299B GLN* 1.3 76.6 - - - +
301B VAL* 1.3 71.4 + - + +
302B ALA 3.2 0.2 + - - -
303B LEU* 3.2 6.9 + - - +
304B ARG* 2.8 38.6 + - + +
333B TYR* 3.6 40.2 - + + -
334B VAL* 3.8 11.9 - - + +
337B GLU* 3.8 27.0 + - + -
573B VAL* 3.8 29.4 + - + +
45M SER* 3.9 18.1 + - - -
46M PRO* 3.9 19.5 - - + -
47M VAL* 4.1 14.0 + - + -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B LEU* 4.0 17.9 - - + -
297B GLU 3.2 8.9 + - - +
298B VAL* 3.1 10.6 + - + +
300B TYR* 1.3 83.6 - - + +
302B ALA* 1.3 64.1 + - - +
304B ARG* 3.2 9.4 + - - +
305B ASN* 3.0 27.3 + - - +
568B GLY 4.7 1.3 - - - +
569B SER 5.6 0.2 - - - +
573B VAL* 4.1 19.3 - - + -
47M VAL* 5.1 1.6 - - + -
75M ALA* 4.1 25.8 - - + +
76M ALA* 4.4 11.4 - - + +
79M PHE* 4.3 22.9 - - + -
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Residues in contact with ALA 302 (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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253B SER* 6.0 0.2 - - - -
257B LEU* 4.1 14.6 - - + +
291B LEU* 3.8 41.3 - - + -
292B LEU* 4.6 6.3 - - + -
298B VAL* 2.8 20.4 + - + +
299B GLN* 3.8 6.3 - - - +
301B VAL* 1.3 72.1 - - - +
303B LEU* 1.3 52.6 + - - +
305B ASN* 2.9 4.9 + - - +
306B ILE* 2.7 39.3 + - + +
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Residues in contact with LEU 303 (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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292B LEU* 3.0 40.8 - - + -
299B GLN* 2.9 25.8 + - + +
300B TYR* 3.5 4.3 - - - +
302B ALA* 1.3 72.4 - - - +
304B ARG* 1.3 55.8 + - - +
305B ASN 3.0 5.4 - - - -
306B ILE* 4.2 1.8 - - - -
307B ASN* 3.0 28.9 + - - +
324B PHE* 3.8 19.1 - - + -
334B VAL* 3.5 37.9 - - + +
337B GLU* 3.8 16.8 - - + +
338B LYS* 3.6 20.9 - - + +
341B ILE* 3.5 11.7 - - + +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B TYR* 2.8 44.6 + - + +
301B VAL* 3.2 10.3 + - - +
303B LEU* 1.3 71.4 - - - +
305B ASN* 1.3 59.6 + - - +
307B ASN* 3.8 9.2 + - - +
308B LEU* 4.1 2.9 - - - +
337B GLU* 3.1 40.3 + - - -
340B ASP* 5.3 2.4 + - - -
572B SER 2.9 16.6 - - - +
573B VAL* 2.5 35.5 + - + +
574B TYR* 3.7 9.1 + - - +
575B HIS* 2.9 64.5 + - - +
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Residues in contact with ASN 305 (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 LEU* 3.3 33.2 - - + +
301B VAL* 3.0 14.7 + - - +
302B ALA* 2.9 11.3 + - - +
304B ARG* 1.3 77.5 - - - +
306B ILE* 1.3 66.0 - - - +
307B ASN 3.2 1.1 - - - -
308B LEU* 3.2 14.6 + - - +
309B ILE* 3.2 25.9 + - + +
567B ILE* 2.5 35.3 + - + +
568B GLY* 4.4 1.2 + - - -
572B SER* 2.6 31.9 - - - +
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Residues in contact with ILE 306 (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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288B LEU* 4.3 35.7 - - + -
291B LEU* 5.9 0.9 - - + -
292B LEU* 3.9 20.2 - - + -
302B ALA* 2.7 24.5 + - + +
303B LEU* 3.8 5.4 - - + +
305B ASN* 1.3 69.4 - - - +
307B ASN* 1.3 66.8 + - - +
309B ILE* 3.4 8.4 - - + +
310B VAL* 2.7 35.4 + - + +
317B LEU* 5.2 4.7 - - + -
324B PHE* 3.3 37.7 - - + -
341B ILE* 3.5 25.1 - - + -
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Residues in contact with ASN 307 (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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303B LEU 3.0 18.4 + - - +
304B ARG* 3.8 12.5 + - - +
306B ILE* 1.3 77.4 - - - +
308B LEU* 1.3 71.9 + - - +
310B VAL* 3.4 8.4 + - - +
311B GLN* 3.4 21.4 + - - +
337B GLU* 4.8 4.3 - - - +
340B ASP* 3.5 31.0 - - - +
341B ILE* 4.0 12.7 - - + +
344B ARG* 3.7 16.3 + - - +
575B HIS* 2.8 32.6 + - + -
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Residues in contact with LEU 308 (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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304B ARG 4.1 3.6 - - - +
305B ASN* 3.2 9.6 + - - +
307B ASN* 1.3 80.7 - - - +
309B ILE* 1.3 58.5 + - - +
311B GLN* 2.5 51.9 + - - +
312B LYS 3.2 6.2 + - - -
555B ILE* 4.4 5.8 - - + -
560B LEU* 4.0 12.1 - - + +
563B LEU* 3.5 46.7 - - + +
564B ILE* 3.7 15.5 - - + -
567B ILE* 5.8 2.5 - - + -
572B SER* 4.3 15.3 - - - -
575B HIS* 3.8 30.7 - - + +
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Residues in contact with ILE 309 (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 LEU* 5.5 1.6 - - + -
260B VAL* 3.6 28.7 - - + -
264B MET* 4.6 12.9 - - - +
288B LEU* 3.9 21.1 - - + -
305B ASN* 3.2 27.6 - - + +
306B ILE* 3.4 7.0 - - - +
308B LEU* 1.3 75.6 - - - +
310B VAL* 1.3 58.3 + - - +
312B LYS* 3.3 1.3 + - - -
313B ARG* 2.8 34.7 + - + +
316B ILE* 5.1 8.5 - - + -
317B LEU* 4.3 21.8 - - + -
564B ILE* 3.1 11.9 - - + +
567B ILE* 4.2 20.9 - - + -
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Residues in contact with VAL 310 (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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306B ILE* 2.7 34.0 + - + +
307B ASN 4.0 0.9 - - - +
308B LEU 2.7 4.4 + - - -
309B ILE* 1.3 69.6 - - - +
311B GLN* 1.3 62.0 + - - +
313B ARG 4.6 0.4 - - - +
314B PRO* 3.4 30.8 - - + +
317B LEU* 4.4 16.6 - - + +
341B ILE* 4.8 3.4 - - + -
344B ARG* 3.7 41.1 - - + +
345B LEU* 3.2 35.2 - - + -
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Residues in contact with GLN 311 (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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307B ASN* 3.4 14.7 + - - +
308B LEU* 2.5 31.8 + - - +
310B VAL* 1.3 73.8 - - - +
312B LYS* 1.3 66.5 + - - +
314B PRO* 3.8 5.5 - - - +
344B ARG* 3.1 42.1 - - - +
554B LEU* 3.5 12.5 - - + +
555B ILE* 2.9 49.5 - - - +
560B LEU* 3.7 14.7 - - + +
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Residues in contact with LYS 312 (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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264B MET* 4.6 8.7 - - + -
308B LEU 3.2 2.2 + - - -
309B ILE 3.8 4.9 - - - +
311B GLN* 1.3 80.7 - - - +
313B ARG* 1.3 100.3 + - + +
314B PRO* 2.8 12.9 - - - +
315B GLU* 4.8 0.2 - - - +
557B PRO 5.3 0.4 + - - -
560B LEU* 3.6 21.4 - - + +
561B ASP* 2.6 34.0 + - - +
564B ILE* 4.2 25.4 - - + -
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Residues in contact with ARG 313 (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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264B MET* 5.2 12.9 + - + +
267B LEU* 4.0 34.1 + - + +
277B TYR* 3.7 26.6 + - - -
281B LEU* 4.8 6.5 - - + -
309B ILE* 2.8 19.4 + - - +
310B VAL* 4.7 2.4 - - - +
312B LYS* 1.3 113.5 + - + +
314B PRO* 1.4 58.0 - - - +
315B GLU* 2.9 37.8 + - - +
316B ILE* 3.3 33.5 + - + +
317B LEU 4.8 0.5 + - - -
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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
------------------------------------------------------------
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