Contacts of the helix formed by residues 39 - 56 (chain B) in PDB entry 3P8P
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 39 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B GLU* 3.3 10.2 + - + +
38B VAL* 1.3 67.7 - - - +
40B VAL* 1.3 59.9 + - - +
41B ALA* 2.6 39.8 + - - +
42B ARG* 2.7 23.2 + - + +
43B ALA* 2.9 20.4 + - - +
264B GLU* 2.9 19.8 + - - +
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Residues in contact with VAL 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 4.0 20.8 - - + +
22B PRO 4.9 0.4 - - - +
23B GLU* 3.2 40.6 - - - +
25B LEU* 4.9 1.8 - - + -
26B GLY* 3.5 33.9 - - - +
38B VAL* 2.7 15.3 + - + +
39B ASP* 1.3 70.8 - - - +
41B ALA* 1.3 55.4 + - - +
43B ALA* 3.9 6.9 - - - +
44B GLU* 2.9 28.0 + - + +
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Residues in contact with ALA 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B ASP* 2.6 20.8 + - - +
40B VAL* 1.3 71.8 - - - +
42B ARG* 1.3 52.6 + - - +
44B GLU* 3.1 8.3 - - - +
45B ARG* 2.7 33.0 + - - +
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Residues in contact with ARG 42 (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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39B ASP* 2.7 30.3 + - + +
41B ALA* 1.3 69.9 - - - +
43B ALA* 1.3 57.8 + - - +
44B GLU 3.0 1.8 - - - -
45B ARG* 3.0 7.9 + - - +
46B GLN* 2.7 44.2 + - + +
264B GLU* 3.8 14.1 - - + +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.5 14.2 - - + +
25B LEU* 5.1 1.3 - - + -
38B VAL* 4.5 7.2 - - + -
39B ASP 2.9 12.9 + - - +
40B VAL* 4.0 8.5 - - - +
42B ARG* 1.3 76.4 - - - +
44B GLU* 1.3 56.4 + - - +
46B GLN* 3.8 6.0 - - - +
47B HIS* 3.1 22.3 + - - +
264B GLU* 3.4 26.7 - - + +
265B LEU* 3.7 26.2 - - + +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LEU* 3.9 28.4 + - + +
40B VAL* 2.9 21.9 + - + +
41B ALA* 3.1 10.3 - - - +
43B ALA* 1.3 75.2 - - - +
45B ARG* 1.3 68.0 + - - +
46B GLN 3.0 2.4 + - - -
47B HIS* 3.0 14.7 + - - +
48B GLN* 3.1 49.6 + - - +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ALA 2.7 21.4 + - - +
42B ARG* 3.0 10.3 + - - +
44B GLU* 1.3 73.5 - - - +
46B GLN* 1.3 60.6 + - + +
48B GLN* 3.7 24.8 + - - +
49B LEU* 3.4 42.2 + - + +
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Residues in contact with GLN 46 (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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42B ARG* 2.7 30.1 + - + +
43B ALA* 3.8 4.8 - - - +
44B GLU 3.0 0.2 - - - -
45B ARG* 1.3 71.8 - - + +
47B HIS* 1.3 64.0 + - - +
48B GLN 3.1 2.0 - - - -
49B LEU* 3.1 15.4 + - + +
50B TYR* 3.1 20.1 + - - +
260B VAL* 5.6 0.3 - - - +
261B SER* 2.7 43.0 + - - +
262B MET* 2.8 34.8 - - + +
263B SER* 2.9 16.1 + - - -
264B GLU* 3.3 18.4 + - - +
265B LEU* 4.2 1.4 + - + +
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.3 14.9 - - + +
19B ARG 3.4 24.6 + - - -
20B ALA* 4.7 5.9 - - - -
21B LEU* 4.2 13.2 + - + -
43B ALA 3.1 16.6 + - - +
44B GLU* 3.0 7.5 + - - +
46B GLN* 1.3 75.5 - - - +
48B GLN* 1.3 65.6 + - + +
50B TYR* 3.2 9.2 + + - +
51B VAL* 3.0 44.3 + - + +
64B GLU* 4.7 5.4 + - - -
75B VAL* 3.4 25.9 - - + +
262B MET* 5.0 4.4 - - - +
265B LEU* 4.6 4.0 - - + -
275B CYS* 4.3 20.6 + - + +
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B GLU* 3.1 33.6 + - - +
45B ARG* 3.7 34.8 + - - +
47B HIS* 1.3 81.0 - - + +
49B LEU* 1.3 56.4 + - - +
51B VAL* 3.6 6.1 + - - +
52B GLY* 2.9 24.4 + - - -
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Residues in contact with LEU 49 (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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45B ARG* 3.4 43.0 + - + +
46B GLN* 3.1 17.7 + - + +
48B GLN* 1.3 75.5 - - - +
50B TYR* 1.3 59.3 + - - +
52B GLY* 3.0 3.0 + - - +
53B VAL* 2.8 35.8 + - + +
260B VAL* 5.5 4.7 - - + -
261B SER* 5.9 6.1 - - - +
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Residues in contact with TYR 50 (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 VAL* 4.2 5.8 - - + -
46B GLN 3.1 11.3 + - - +
47B HIS* 3.3 16.2 - + - +
49B LEU* 1.3 75.1 - - - +
51B VAL* 1.3 66.8 + - + +
53B VAL* 3.0 16.1 + - - +
54B LEU* 3.0 41.8 + - + +
223B ILE* 3.5 8.2 - - + +
235B LEU* 5.6 6.2 - - + +
260B VAL* 4.3 12.5 - - + +
262B MET* 4.2 15.7 - - + -
272B LEU* 2.2 60.6 + - + -
275B CYS* 3.6 26.5 - - + -
276B SER* 2.8 31.3 + - - -
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Residues in contact with VAL 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 4.1 18.8 - - + -
47B HIS* 3.0 39.3 + - + +
48B GLN* 3.9 5.8 - - - +
50B TYR* 1.3 82.0 - - + +
52B GLY* 1.3 63.7 + - - +
54B LEU* 3.6 8.0 - - - +
55B GLY* 2.9 23.1 + - - -
56B SER* 4.1 1.5 + - - +
62B VAL* 3.7 27.1 - - + -
64B GLU* 4.1 16.8 - - + +
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Residues in contact with GLY 52 (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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48B GLN 2.9 16.9 + - - -
49B LEU* 3.3 5.6 - - - -
50B TYR 3.0 0.2 - - - -
51B VAL* 1.3 77.1 - - - +
53B VAL* 1.3 57.7 + - - +
56B SER* 2.9 23.6 + - - -
57B LYS* 2.9 25.0 + - - -
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Residues in contact with VAL 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LEU* 2.8 21.7 + - + +
50B TYR* 3.0 8.5 + - - +
52B GLY* 1.3 72.9 - - - +
54B LEU* 1.3 56.5 + - - +
57B LYS* 3.3 12.2 - - + +
58B LEU* 2.9 31.9 + - + +
235B LEU* 3.4 35.4 - - + -
258B ILE* 4.0 33.7 - - + -
259B PRO 5.7 0.4 - - - +
260B VAL* 4.7 8.7 - - + -
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Residues in contact with LEU 54 (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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16B ALA* 4.1 16.6 - - + -
18B VAL* 4.6 4.9 - - + -
50B TYR* 3.0 45.0 + - + +
51B VAL* 3.6 8.5 - - + +
52B GLY 3.2 0.2 - - - -
53B VAL* 1.3 77.2 - - - +
55B GLY* 1.3 59.2 + - - +
58B LEU* 3.3 20.4 - - + +
60B LEU* 3.0 34.3 + - + +
62B VAL* 4.3 8.3 - - + -
223B ILE* 5.6 3.6 - - + -
225B LEU* 5.0 7.2 - - + -
235B LEU* 3.9 25.8 - - + -
276B SER* 4.0 15.7 - - - +
278B LEU* 5.1 5.2 - - + -
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Residues in contact with GLY 55 (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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51B VAL 2.9 12.7 + - - -
54B LEU* 1.3 75.6 - - - +
56B SER* 1.3 63.2 + - - +
59B GLY* 3.0 25.3 + - - -
60B LEU 3.2 19.0 - - - +
62B VAL* 3.3 14.7 - - - +
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Residues in contact with SER 56 (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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51B VAL* 4.1 1.6 + - - +
52B GLY* 2.9 19.6 + - - -
55B GLY* 1.3 78.4 - - - +
57B LYS* 1.3 64.8 + - - +
59B GLY* 4.1 2.9 + - - -
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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