Contacts of the helix formed by residues 21 - 42 (chain V) in PDB entry 2W5J
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 SER 21 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M LEU 3.2 12.5 + - - -
20M ALA* 3.2 22.4 - - - -
24M PRO* 2.9 23.7 - - - +
63M LEU* 3.5 25.4 + - - +
18V GLY* 3.8 11.6 + - - -
19V LEU 3.0 0.6 - - - -
20V ALA* 1.3 77.9 - - - +
22V ILE* 1.3 71.5 + - - +
25V GLY* 2.8 22.0 + - - -
64V THR* 4.8 0.2 - - - -
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Residues in contact with ILE 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 5.6 5.2 - - + -
19M LEU* 4.8 3.3 + - + +
22M ILE* 5.6 3.8 - - + -
23M GLY* 3.5 19.1 - - - +
18V GLY 4.3 1.9 + - - +
19V LEU* 3.0 18.6 + - + +
21V SER* 1.3 85.3 + - - +
23V GLY* 1.3 67.3 + - - +
25V GLY* 3.0 5.4 + - - -
26V VAL* 3.2 12.1 + - - +
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Residues in contact with GLY 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 3.7 6.8 + - - -
22A ILE* 3.6 26.2 - - - +
25A GLY* 3.3 12.9 - - - -
26A VAL* 3.4 6.4 + - - +
19V LEU 3.8 0.2 + - - -
22V ILE* 1.3 78.9 - - - +
24V PRO* 1.3 71.8 - - - +
26V VAL* 3.3 7.4 + - - +
27V GLY 3.1 15.1 + - - -
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Residues in contact with PRO 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER* 2.9 24.2 - - - +
25A GLY* 3.5 10.5 - - - +
63M LEU* 3.8 5.8 - - + -
20V ALA 3.4 5.4 - - - +
22V ILE 3.8 0.4 - - - -
23V GLY* 1.3 82.4 - - - +
25V GLY* 1.3 60.0 + - - +
27V GLY* 2.5 28.9 + - - -
28V GLN* 3.3 10.1 + - + +
60V MET* 3.9 16.4 - - + +
63V LEU* 3.2 23.6 - - + -
64V THR* 3.1 34.3 - - + -
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Residues in contact with GLY 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M GLY 3.3 7.6 - - - +
24M PRO* 3.4 25.1 - - - +
27M GLY* 3.4 16.1 - - - -
28M GLN 4.5 0.7 + - - -
60M MET* 5.5 3.5 - - - +
63M LEU* 4.2 7.0 - - - +
21V SER 2.8 24.9 + - - -
24V PRO* 1.3 72.4 - - - +
26V VAL* 1.3 62.8 + - - +
28V GLN* 5.5 0.6 - - - +
29V GLY* 4.0 7.3 + - - -
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Residues in contact with VAL 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL* 3.8 25.6 - - + -
23M GLY* 3.4 11.2 + - - +
26M VAL* 3.8 27.5 - - + +
27M GLY* 4.1 7.2 - - - -
30M THR* 5.7 0.2 - - - +
22V ILE 3.2 8.2 + - - +
23V GLY 3.4 8.3 - - - +
24V PRO 2.8 3.6 + - - -
25V GLY* 1.3 77.0 - - - +
27V GLY* 1.3 70.0 + - - +
29V GLY* 3.7 2.1 + - - -
30V THR* 3.1 24.3 + - + +
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Residues in contact with GLY 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 3.4 18.4 - - - -
26A VAL 4.2 7.4 - - - -
29A GLY* 4.2 5.8 - - - -
23V GLY 3.1 3.4 + - - -
24V PRO 2.5 11.5 + - - -
26V VAL* 1.3 72.8 - - - +
28V GLN* 1.3 54.5 + - - -
29V GLY 2.9 1.8 - - - -
30V THR* 2.3 50.4 + - - +
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Residues in contact with GLN 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLY 4.6 0.4 + - - -
29A GLY* 4.2 6.7 - - - -
56M SER* 6.2 0.2 - - - -
59M PHE* 5.4 7.2 - - + +
60M MET* 6.5 0.9 - - - -
63M LEU* 6.4 1.1 - - + -
24V PRO 3.3 9.8 + - - +
25V GLY 5.5 0.2 - - - +
27V GLY* 1.3 65.9 - - - -
29V GLY* 1.3 52.0 + - - +
31V ALA* 2.9 14.7 + - - +
32V ALA* 2.7 35.9 + - - +
57V LEU* 3.9 20.8 - - + +
60V MET* 3.6 29.5 - - + +
61V GLU* 6.3 0.4 - - + -
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Residues in contact with GLY 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M GLY 4.2 0.4 - - - -
28M GLN* 4.1 22.4 - - - -
30M THR* 2.9 20.2 + - - -
31M ALA* 3.6 6.1 - - - +
56M SER* 6.0 0.4 - - - -
60M MET* 5.9 3.9 - - - +
25V GLY 4.0 6.4 + - - -
26V VAL 3.7 7.0 + - - -
27V GLY 2.6 6.2 + - - -
28V GLN* 1.3 74.6 - - - +
30V THR* 1.3 54.3 + - - -
32V ALA* 4.3 6.7 - - - -
33V GLY 3.1 16.3 + - - -
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Residues in contact with THR 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A VAL 5.7 1.3 - - - +
29A GLY 2.8 21.7 + - - -
30A THR* 4.1 7.8 + - + +
33A GLY* 4.7 1.4 - - - -
30M THR* 4.2 9.6 - - + +
26V VAL* 3.1 21.5 - - + +
27V GLY* 2.3 32.7 + - - +
29V GLY 1.3 65.5 - - - -
31V ALA* 1.3 64.8 + - - -
32V ALA 3.3 0.2 - - - -
33V GLY* 3.1 1.0 + - - -
34V GLN* 2.5 40.8 + - - +
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Residues in contact with ALA 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 3.6 13.0 - - - +
32A ALA* 3.8 20.4 - - + -
33A GLY* 3.7 14.4 - - - +
36A VAL* 3.9 3.4 - - + +
27V GLY 3.4 0.4 + - - -
28V GLN* 2.9 14.1 + - - +
30V THR* 1.3 82.2 + - - +
32V ALA* 1.3 64.9 + - - +
34V GLN* 3.1 1.6 + - - +
35V ALA* 2.8 26.5 + - - +
53V LEU* 4.9 4.7 - - - -
56V SER* 5.1 1.1 - - - -
57V LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M ALA* 3.9 10.1 - - + -
52M THR* 5.6 0.2 - - - +
53M LEU* 5.9 1.1 - - - -
56M SER* 3.1 37.2 - - - +
28V GLN 2.7 18.6 + - - +
29V GLY* 3.8 8.1 - - - +
31V ALA* 1.3 71.0 - - - +
33V GLY* 1.3 64.8 + - - +
35V ALA* 2.9 4.7 + - - +
36V VAL* 2.9 25.8 + - - +
53V LEU* 3.8 15.3 - - + +
57V LEU* 4.3 2.3 - - + +
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Residues in contact with GLY 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M THR* 4.7 1.1 - - - -
31M ALA* 3.6 22.9 - - - +
34M GLN* 3.5 17.7 - - - +
29V GLY 3.1 8.0 + - - -
30V THR* 3.1 6.3 + - - -
32V ALA* 1.3 79.2 - - - +
34V GLN* 1.3 59.5 + - - +
36V VAL* 2.9 25.3 - - - +
37V GLU* 3.4 5.4 + - - +
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Residues in contact with GLN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLY* 3.4 31.9 - - - +
36A VAL* 3.5 7.7 - - - +
37A GLU* 4.0 15.1 - - + +
30V THR* 2.5 20.3 + - - +
33V GLY* 1.3 71.0 - - - +
35V ALA* 1.3 59.0 + - - +
37V GLU* 4.3 5.0 - - - +
38V GLY* 3.6 13.0 + - - -
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Residues in contact with ALA 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 3.1 32.7 - - + +
52M THR* 5.2 2.2 - - + -
31V ALA 2.8 15.5 + - - +
32V ALA 3.5 3.6 - - - +
34V GLN* 1.3 75.6 - - - +
36V VAL* 1.3 66.6 + - - +
37V GLU 3.2 1.6 - - - -
38V GLY* 3.0 3.0 + - - -
39V ILE* 2.9 29.8 + - + +
49V ILE* 4.9 4.7 - - + -
53V LEU* 3.9 22.0 - - + -
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Residues in contact with VAL 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31M ALA* 4.0 2.7 - - + +
34M GLN 3.7 1.1 - - - -
35M ALA* 3.2 49.5 - - + +
38M GLY* 5.4 0.3 - - - -
49M ILE* 3.7 35.9 - - + +
52M THR* 5.2 8.9 - - - +
53M LEU* 4.9 8.3 - - + +
32V ALA 2.9 10.6 + - - +
33V GLY* 2.9 28.5 - - - +
35V ALA* 1.3 76.9 - - - +
37V GLU* 1.3 60.7 + - - +
39V ILE* 3.7 7.5 + - - +
40V ALA* 3.2 19.1 + - - +
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Residues in contact with GLU 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34M GLN* 4.1 17.7 - - + +
38M GLY* 5.0 3.8 - - - -
41M ARG* 6.2 2.2 - - - +
33V GLY 3.4 9.8 + - - +
34V GLN* 4.5 4.9 - - - +
35V ALA 3.2 0.4 - - - -
36V VAL* 1.3 80.5 - - - +
38V GLY* 1.3 58.1 + - - +
40V ALA* 2.7 34.6 + - - +
41V ARG* 3.0 13.0 + - - +
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Residues in contact with GLY 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL 5.3 0.4 - - - -
37A GLU* 5.0 4.0 - - - -
40A ALA* 3.6 30.3 - - - +
34V GLN 3.6 10.7 + - - -
35V ALA* 3.0 6.6 + - - -
37V GLU* 1.3 78.0 - - - +
39V ILE* 1.3 62.5 + - - +
41V ARG* 3.0 25.1 + - - +
42V GLN* 3.2 11.4 + - - +
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Residues in contact with ILE 39 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A VAL* 5.6 0.4 - - + +
40A ALA* 5.4 4.7 - - + -
45M ALA* 5.7 1.1 - - + +
48M LYS* 3.8 29.4 - - + +
49M ILE* 4.9 1.1 - - - +
52M THR* 5.3 7.2 - - + +
35V ALA* 2.9 21.7 + - + +
36V VAL* 3.9 7.4 - - - +
38V GLY* 1.3 72.9 - - - +
40V ALA* 1.3 67.8 + - - +
41V ARG 3.1 0.7 + - - -
42V GLN 4.2 3.6 - - - +
43V PRO* 3.2 27.5 - - + +
45V ALA* 4.2 4.3 - - + +
46V GLU* 3.6 42.2 - - + +
49V ILE* 2.9 36.6 - - + -
50V ARG* 6.0 1.8 - - + -
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Residues in contact with ALA 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M GLY* 3.7 36.3 - - - +
39M ILE* 4.7 5.2 - - + +
41M ARG* 6.0 2.0 - - - +
42M GLN* 3.4 22.9 - - - +
45M ALA* 4.2 10.9 - - + +
49M ILE* 6.1 1.1 - - - +
36V VAL 3.2 14.5 + - - +
37V GLU 2.7 21.0 + - - +
39V ILE* 1.3 73.0 - - - +
41V ARG* 1.3 61.0 + - - +
43V PRO* 3.8 8.7 - - - +
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Residues in contact with ARG 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A GLU* 6.1 3.2 - - - +
40A ALA* 5.6 3.3 - - + +
41A ARG* 4.6 23.3 - - - +
41M ARG* 4.6 22.3 - - - +
42M GLN* 4.5 14.3 + - - +
37V GLU* 3.0 9.8 + - - +
38V GLY* 3.0 22.6 + - - +
40V ALA* 1.3 81.3 - - - +
42V GLN* 1.3 85.4 + - - +
43V PRO* 3.2 6.9 - - - +
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Residues in contact with GLN 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ALA* 3.1 30.7 - - - +
41A ARG* 4.4 12.4 + - - +
43A PRO* 5.5 2.5 - - + -
38V GLY 3.2 6.0 + - - +
39V ILE* 3.3 8.5 - - - +
41V ARG* 1.3 107.8 + - - +
43V PRO* 1.4 60.9 - - - +
44V GLU* 3.3 3.8 - - + +
45V ALA* 3.0 29.3 + - + +
46V GLU 3.7 2.4 + - - -
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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
------------------------------------------------------------
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