Contacts of the helix formed by residues 307 - 317 (chain B) in PDB entry 2VR1
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 ASP 307 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A PHE* 3.7 12.0 - - + +
393A GLU* 5.2 6.0 + - - +
401A ARG* 3.1 22.8 + - - +
16B ARG* 3.1 28.3 + - - -
20B ALA* 5.2 0.3 - - - +
23B GLU* 4.2 3.5 - - - +
301B GLU* 3.6 2.7 - - - -
305B GLY 3.8 3.6 + - - +
306B VAL* 1.3 73.2 - - - +
308B LEU* 1.3 61.0 + - - +
309B ILE* 3.3 0.9 + - - +
310B LYS* 2.8 55.8 + - + +
311B GLU* 2.9 26.4 + - - +
314B ARG* 5.4 2.5 - - - +
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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
----------------------------------------------------------
213B GLN* 3.9 39.9 - - + +
215B LEU* 4.2 23.4 - - + +
225B LEU* 4.3 7.4 - - + -
272B ALA* 5.1 1.5 - - + +
293B ILE* 3.9 13.7 - - + -
297B HIS* 3.6 38.8 - - + +
300B THR* 4.3 8.3 - - + -
301B GLU* 2.7 24.2 + - + +
306B VAL* 3.3 14.8 + - + +
307B ASP* 1.3 71.7 - - - +
309B ILE* 1.3 56.7 + - - +
311B GLU* 3.4 6.1 + - - +
312B GLN* 3.0 30.6 + - - +
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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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13B ILE* 4.9 0.9 - - + -
16B ARG* 3.5 35.9 - - + +
17B ILE* 4.2 23.3 - - + -
20B ALA* 3.5 23.3 - - + -
79B HIS* 4.5 7.2 - - + +
293B ILE* 3.8 26.5 - - + -
297B HIS* 4.1 11.9 - - + +
301B GLU* 3.8 0.2 + - - -
307B ASP* 3.3 5.1 + - - +
308B LEU* 1.3 73.5 - - - +
310B LYS* 1.3 65.1 + - - +
312B GLN* 3.1 31.7 + - - +
313B LEU* 3.1 20.0 + - + +
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Residues in contact with LYS 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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393A GLU* 3.6 20.6 + - - -
397A VAL* 3.6 22.4 - - - +
401A ARG* 3.8 2.7 - - - +
20B ALA* 3.9 12.6 - - + -
23B GLU* 3.0 32.8 + - + +
24B LEU* 3.9 40.3 - - + +
307B ASP* 2.8 47.3 + - + +
309B ILE* 1.3 72.3 - - - +
311B GLU* 1.3 56.5 + - - +
313B LEU* 3.2 5.6 + - - +
314B ARG* 2.9 50.4 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.9 23.5 - - + +
306B VAL* 3.8 23.3 - - + +
307B ASP 2.9 18.3 + - - +
308B LEU 3.5 8.1 - - - +
310B LYS* 1.3 74.9 - - - +
312B GLN* 1.3 65.1 + - - +
314B ARG* 2.9 38.8 + - - +
315B ILE* 3.0 30.9 + - + +
321B LEU* 5.0 9.0 - - - +
322B SER* 4.3 13.6 + - - -
323B ILE* 4.8 15.7 - - - +
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Residues in contact with GLN 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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79B HIS* 2.9 33.7 + - - +
103B ILE* 4.0 22.3 + - + +
104B GLY* 5.7 2.6 - - - -
215B LEU* 4.9 0.4 - - + +
271B GLY* 5.4 2.2 - - - -
272B ALA* 3.9 26.0 + - + +
292B ARG* 4.7 2.0 - - - +
293B ILE* 3.8 33.2 - - - +
308B LEU 3.0 16.8 + - - +
309B ILE* 3.1 28.6 + - - +
311B GLU* 1.3 74.8 - - - +
313B LEU* 1.3 59.1 + - + +
315B ILE* 3.2 9.9 + - - +
316B ALA* 3.0 30.1 + - - +
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Residues in contact with LEU 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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1B MET* 4.6 3.2 - - - +
2B LEU* 4.2 12.1 - - + +
5B ILE* 4.3 12.1 - - + -
17B ILE* 5.2 0.2 - - + -
20B ALA* 3.9 20.6 - - + -
21B CYS* 4.3 9.6 - - - +
24B LEU* 3.7 26.7 - - + -
26B ILE* 4.0 17.3 - - + -
79B HIS* 4.2 15.3 - - + -
103B ILE* 3.7 27.8 - - + -
309B ILE* 3.1 19.4 + - + +
310B LYS 3.6 4.5 - - - +
312B GLN* 1.3 77.1 - - + +
314B ARG* 1.3 62.3 + - - +
316B ALA* 3.5 4.9 + - - +
317B ALA* 3.0 24.3 + - - +
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Residues in contact with ARG 314 (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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393A GLU* 4.7 11.5 + - - -
397A VAL* 5.5 3.8 - - - +
1B MET* 4.4 19.3 - - + +
24B LEU* 4.1 21.2 - - + +
307B ASP* 5.2 1.6 + - - +
310B LYS* 2.9 45.8 + - - +
311B GLU* 2.9 46.4 + - - +
312B GLN 3.3 0.2 - - - -
313B LEU* 1.3 76.4 - - - +
315B ILE* 1.3 61.9 + - + +
317B ALA* 3.3 12.8 + - - +
319B GLN* 3.2 46.5 + - + +
322B SER* 5.4 5.8 + - - -
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Residues in contact with ILE 315 (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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215B LEU* 4.0 19.1 - - + -
216B ALA 3.4 22.4 - - - +
217B ASP* 4.0 16.9 - - - +
219B GLN* 5.1 1.0 + - - -
270B ARG* 4.0 29.0 - - + -
271B GLY* 4.0 12.1 - - - +
311B GLU* 3.0 24.6 + - + +
312B GLN* 3.2 4.9 + - - +
314B ARG* 1.3 75.5 - - + +
316B ALA* 1.3 58.8 + - - +
318B GLY* 2.6 28.1 + - - -
319B GLN 3.8 12.1 + - - +
320B PRO 5.7 0.2 - - - -
321B LEU* 3.9 23.6 - - + +
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Residues in contact with ALA 316 (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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2B LEU* 4.7 3.8 - - + -
101B ILE* 3.5 43.4 - - + +
102B PHE 4.6 1.6 - - - +
103B ILE* 3.8 29.8 - - + -
104B GLY 5.3 0.9 - - - +
270B ARG* 6.0 5.2 - - - +
312B GLN 3.0 16.3 + - - +
313B LEU* 4.0 4.5 - - - +
315B ILE* 1.3 78.3 - - - +
317B ALA* 1.3 57.2 + - - +
318B GLY* 3.2 5.0 + - - -
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Residues in contact with ALA 317 (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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1B MET* 4.3 29.4 - - - +
2B LEU* 4.2 17.3 - - + +
101B ILE* 5.0 2.0 - - - -
313B LEU 3.0 15.4 + - - +
314B ARG* 3.4 12.8 - - - +
315B ILE 3.1 0.4 - - - -
316B ALA* 1.3 74.2 - - - +
318B GLY* 1.3 57.8 + - - -
319B GLN* 3.3 10.9 + - + +
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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