Contacts of the helix formed by residues 20 - 31 (chain B) in PDB entry 1RFV
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 20 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B GLN* 3.5 24.7 - - - +
12B SER* 3.8 14.1 - - - -
19B VAL* 1.3 73.3 - - - +
21B ASN* 1.3 63.0 + - - -
23B ALA* 3.0 13.3 + - - +
24B ALA* 3.1 12.5 + - - +
235B ASP* 2.8 22.0 + - - +
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Residues in contact with ASN 21 (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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9B SER* 2.5 40.6 + - - +
11B GLN* 3.3 17.8 - - - +
12B SER 2.8 19.0 + - - +
13B HIS* 5.0 2.5 - - + +
20B GLY* 1.3 71.4 - - - -
22B ARG* 1.3 57.6 + - - +
23B ALA 3.3 0.2 - - - -
24B ALA* 3.7 3.4 - - - +
25B THR* 2.8 40.7 + - - +
37B ALA* 3.6 12.7 - - + +
38B VAL 3.1 24.1 - - - +
39B ASN* 3.4 15.7 - - - +
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Residues in contact with ARG 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A THR* 5.0 4.6 - - - +
29A GLN* 4.9 9.3 + - - +
34A GLU* 4.7 0.6 + - - -
35A VAL* 2.8 30.9 + - - +
36A ASP* 4.2 3.0 + - - -
37A ALA* 3.8 20.8 - - - +
12B SER 4.2 0.4 + - - -
13B HIS* 3.7 22.0 - - + +
14B VAL* 3.5 29.0 + - + +
15B VAL 3.7 13.3 + - - -
17B GLY 3.0 34.3 + - - +
18B TYR* 3.4 40.9 + - - -
19B VAL 3.0 14.5 + - - +
21B ASN* 1.3 78.8 - - - +
23B ALA* 1.3 60.2 + - - +
25B THR* 4.4 3.4 + - - -
26B PHE* 4.5 11.1 + - - +
27B PRO* 4.9 0.3 - - - +
293B MET* 5.0 0.2 - - - +
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Residues in contact with ALA 23 (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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18B TYR* 4.0 8.3 - - + +
19B VAL* 3.6 18.9 + - - +
20B GLY 3.0 9.0 + - - +
22B ARG* 1.3 78.6 - - - +
24B ALA* 1.3 58.9 + - - +
27B PRO* 3.2 22.9 - - - +
232B GLY 3.8 22.0 - - - +
235B ASP* 4.1 5.8 - - + -
236B LEU* 3.6 16.1 - - - +
291B LEU* 5.1 0.4 - - + -
293B MET* 4.1 14.3 - - + +
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Residues in contact with ALA 24 (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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9B SER* 4.6 4.3 - - - +
11B GLN* 3.8 21.1 - - - +
20B GLY 3.1 12.9 + - - +
21B ASN* 3.5 4.5 + - - +
22B ARG 3.4 0.2 - - - -
23B ALA* 1.3 80.7 - - - +
25B THR* 1.3 66.4 + - - +
27B PRO* 3.5 1.8 - - - +
28B LEU* 3.4 28.4 + - + +
81B LEU* 4.2 7.6 - - + -
235B ASP 4.6 5.4 - - - +
239B ALA* 3.7 21.0 - - + +
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Residues in contact with THR 25 (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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22A ARG* 5.0 7.4 - - - +
21B ASN* 2.8 31.2 + - - +
22B ARG* 4.4 1.3 + - - -
24B ALA* 1.3 75.7 - - - +
26B PHE* 1.3 67.4 + - - +
28B LEU* 3.2 3.3 + - - +
29B GLN* 2.9 57.7 + - + +
35B VAL* 4.1 26.3 - - + +
37B ALA* 4.3 8.3 - - + +
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Residues in contact with PHE 26 (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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26A PHE* 4.5 7.0 - + - -
29A GLN* 3.4 58.3 + - + +
30A VAL* 4.1 11.2 - - + -
22B ARG 4.5 6.6 + - - +
25B THR* 1.3 75.3 - - - +
27B PRO* 1.3 73.0 - - + +
29B GLN* 3.2 8.6 + - - +
30B VAL* 3.0 50.4 + - + +
293B MET* 3.7 43.5 - - + -
294B VAL* 4.2 8.1 - - + -
297B LYS* 4.2 26.5 - - + -
300B ILE* 4.8 4.3 - - + -
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Residues in contact with PRO 27 (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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23B ALA 3.2 27.8 - - - +
24B ALA 3.5 4.7 - - - +
25B THR 3.5 3.6 - - - -
26B PHE* 1.3 96.8 - - + +
28B LEU* 1.3 61.2 - - - +
30B VAL* 3.2 12.7 - - + +
31B LEU* 3.1 28.6 + - - +
236B LEU* 3.5 21.5 - - + -
239B ALA* 5.0 4.3 - - + -
240B MET* 4.4 11.2 - - + +
293B MET* 3.7 13.2 - - - -
300B ILE* 4.1 17.0 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 4.3 16.4 - - + -
9B SER* 5.7 0.7 - - - -
24B ALA* 3.4 19.7 + - + +
25B THR 3.2 1.4 + - - -
27B PRO* 1.3 80.8 - - - +
29B GLN* 1.3 59.9 + - - +
31B LEU* 3.3 3.1 + - + -
32B GLY 3.2 5.2 + - - -
33B PHE* 2.8 52.2 + - + +
35B VAL* 3.6 26.5 - - + -
81B LEU* 4.3 23.8 - - + -
239B ALA* 3.3 27.8 - - + +
242B LEU* 4.5 7.9 - - + -
243B ALA* 4.1 13.7 - - + +
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Residues in contact with GLN 29 (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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18A TYR* 4.3 22.8 + - - -
22A ARG* 4.9 8.1 + - - +
26A PHE* 3.4 46.4 + - + +
29A GLN* 4.3 5.9 - - - +
294A VAL* 3.4 27.7 - - + +
297A LYS* 5.2 0.7 - - - +
25B THR* 2.9 44.0 + - + +
26B PHE* 3.2 9.3 + - - +
28B LEU* 1.3 74.1 - - - +
30B VAL* 1.3 65.5 + - - +
32B GLY 3.0 10.7 + - - -
33B PHE 3.8 6.5 - - - -
35B VAL* 4.1 13.6 + - + +
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Residues in contact with VAL 30 (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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26A PHE* 4.1 7.9 - - + -
30A VAL* 4.7 0.7 - - + -
297A LYS* 3.1 31.2 + - + -
26B PHE* 3.0 53.6 + - + +
27B PRO* 3.2 16.2 - - + +
29B GLN* 1.3 76.4 - - - +
31B LEU* 1.3 59.9 + - + +
32B GLY 3.2 1.8 + - - -
297B LYS* 4.2 12.1 - - + +
300B ILE* 3.9 23.8 - - + -
301B GLU* 4.1 24.5 - - + +
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Residues in contact with LEU 31 (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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27B PRO 3.1 25.0 + - - +
28B LEU* 3.7 6.1 - - - +
29B GLN 3.1 0.6 - - - -
30B VAL* 1.3 77.1 - - + +
32B GLY* 1.3 59.0 + - - +
33B PHE* 3.6 19.2 - - + -
240B MET* 4.9 10.1 - - + -
243B ALA* 3.4 26.5 - - + -
244B TRP* 3.8 28.3 - - + +
300B ILE* 3.6 33.9 - - + +
301B GLU* 4.0 11.7 - - - +
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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