Contacts of the helix formed by residues 21 - 42 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU 3.2 12.5 + - - -
20G ALA* 3.4 21.0 - - - -
23G GLY 3.8 0.2 + - - -
24G PRO* 2.9 23.5 - - - +
63G LEU* 3.7 24.8 + - - +
18H GLY* 3.8 11.7 + - - -
19H LEU 2.9 0.2 - - - -
20H ALA* 1.3 78.8 - - - +
22H ILE* 1.3 70.0 + - - +
25H GLY* 2.8 24.6 + - - -
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 4.9 1.8 + - + +
22G ILE* 5.7 3.8 - - + -
23G GLY* 3.6 18.6 - - - +
18H GLY 4.4 1.3 + - - +
19H LEU* 2.9 20.1 + - + +
21H SER* 1.3 83.9 + - - +
23H GLY* 1.3 68.9 + - - +
25H GLY* 3.1 5.2 + - - -
26H VAL* 3.2 13.1 + - - +
22I ILE* 5.5 6.1 - - + -
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Residues in contact with GLY 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19H LEU 3.8 0.4 + - - -
22H ILE* 1.3 81.7 - - - +
24H PRO* 1.4 70.2 - - - +
26H VAL* 3.2 6.6 + - - +
27H GLY 3.1 15.1 + - - -
21I SER* 3.7 4.0 + - - -
22I ILE* 3.5 28.9 - - - +
25I GLY* 3.3 11.4 - - - -
26I VAL* 3.4 7.0 + - - -
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Residues in contact with PRO 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU* 3.9 6.1 - - + -
20H ALA 3.5 4.9 - - - +
22H ILE 3.8 0.4 - - - -
23H GLY* 1.4 81.8 - - - +
25H GLY* 1.3 59.0 + - - +
27H GLY* 2.6 28.6 + - - -
28H GLN* 3.3 10.5 + - + +
60H MET* 3.9 17.9 - - + +
63H LEU* 3.1 23.1 - - + -
64H THR* 3.1 34.1 - - + -
21I SER* 2.9 23.6 - - - +
25I GLY* 3.4 11.6 - - - +
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Residues in contact with GLY 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLY 3.4 7.6 - - - -
24G PRO* 3.5 25.1 - - - +
27G GLY* 3.4 16.3 - - - -
28G GLN 4.5 0.7 + - - -
60G MET* 5.5 4.0 - - - +
63G LEU* 4.3 6.9 - - - +
21H SER 2.8 26.2 + - - -
24H PRO* 1.3 72.3 - - - +
26H VAL* 1.3 62.2 + - - +
28H GLN* 6.0 0.4 - - - -
29H GLY* 4.0 7.3 + - - -
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Residues in contact with VAL 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLY* 3.5 10.2 + - - +
26G VAL* 3.9 25.1 - - + +
27G GLY* 4.1 8.0 - - - -
30G THR* 5.8 0.2 - - - +
22H ILE 3.2 10.3 + - - +
23H GLY 3.4 7.6 - - - +
24H PRO 2.8 3.0 + - - -
25H GLY* 1.3 76.1 - - - +
27H GLY* 1.3 68.7 + - - +
29H GLY* 3.6 1.7 + - - -
30H THR* 3.1 23.7 + - + +
26I VAL* 3.8 26.5 - - + +
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Residues in contact with GLY 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23H GLY 3.1 4.2 + - - -
24H PRO 2.6 11.7 + - - -
26H VAL* 1.3 72.0 - - - +
28H GLN* 1.3 54.1 + - - -
29H GLY 2.9 2.7 - - - -
30H THR* 2.4 50.8 + - - +
25I GLY 3.4 17.9 - - - -
26I VAL 4.1 8.5 - - - -
29I GLY* 4.1 6.1 - - - -
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Residues in contact with GLN 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G PHE* 5.5 7.4 - - + +
60G MET* 6.6 0.2 - - - -
63G LEU* 6.6 0.2 - - + -
24H PRO* 3.3 9.8 + - + +
25H GLY* 5.5 0.4 - - - +
27H GLY* 1.3 67.2 - - - -
29H GLY* 1.3 51.8 + - - +
31H ALA* 2.9 15.1 + - - +
32H ALA* 2.7 35.6 + - - +
57H LEU* 4.0 21.2 - - + +
60H MET* 3.6 29.3 - - + +
61H GLU* 6.3 0.7 - - + -
25I GLY 4.5 0.6 + - - -
29I GLY* 4.1 6.8 - - - -
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Residues in contact with GLY 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G GLY 4.2 17.3 - - - -
28G GLN* 4.2 4.0 - - - -
30G THR* 2.9 20.6 + - - -
31G ALA* 3.5 7.0 - - - +
56G SER* 6.1 0.4 - - - -
60G MET* 6.0 3.5 - - - +
25H GLY 4.0 5.9 + - - -
26H VAL 3.6 8.2 + - - -
27H GLY 2.5 7.0 + - - -
28H GLN* 1.3 73.8 - - - +
30H THR* 1.3 54.6 + - - -
32H ALA* 4.3 6.3 - - - -
33H GLY 3.1 16.8 + - - -
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Residues in contact with THR 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G THR* 4.2 10.1 - - + +
26H VAL* 3.1 20.0 - - + +
27H GLY* 2.4 34.7 + - - +
29H GLY* 1.3 65.8 - - - -
31H ALA* 1.3 67.1 + - - -
33H GLY* 3.0 1.1 + - - -
34H GLN* 2.5 40.3 + - - +
26I VAL 5.7 1.1 - - - +
29I GLY 2.7 21.8 + - - -
30I THR* 4.1 9.1 + - + -
33I GLY* 4.6 1.8 - - - -
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Residues in contact with ALA 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27H GLY 3.4 0.6 + - - -
28H GLN* 2.9 14.5 + - - +
30H THR* 1.3 82.9 + - - +
32H ALA* 1.3 64.4 + - - +
34H GLN* 3.0 1.4 + - - +
35H ALA* 2.8 26.4 + - - +
53H LEU* 4.8 4.3 - - - -
56H SER* 5.1 0.9 - - - -
57H LEU* 4.0 14.8 - - + -
29I GLY 3.6 12.3 - - - +
32I ALA* 3.8 20.6 - - + -
33I GLY* 3.7 13.5 - - - +
36I VAL* 3.9 3.0 - - + +
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Residues in contact with ALA 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ALA* 3.8 10.8 - - + -
52G THR* 5.5 0.8 - - - +
53G LEU* 5.9 1.3 - - - -
56G SER* 3.2 35.2 - - - +
28H GLN 2.7 18.2 + - - +
29H GLY* 3.8 8.1 - - - +
31H ALA* 1.3 74.0 - - - +
33H GLY* 1.3 65.2 + - - +
35H ALA* 2.9 1.7 + - - +
36H VAL* 2.9 26.6 + - - +
53H LEU* 3.8 15.7 - - + +
57H LEU* 4.3 3.4 - - + +
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Residues in contact with GLY 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G THR* 4.7 1.3 - - - -
31G ALA* 3.7 22.8 - - - +
34G GLN* 3.4 20.1 - - - +
29H GLY 3.1 7.0 + - - -
30H THR* 3.0 6.8 + - - -
32H ALA* 1.3 79.4 - - - +
34H GLN* 1.3 58.3 + - - +
36H VAL* 2.9 22.6 - - - +
37H GLU* 3.4 6.2 + - - +
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Residues in contact with GLN 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H THR* 2.5 20.9 + - - +
33H GLY* 1.3 71.7 - - - +
35H ALA* 1.3 59.1 + - - +
37H GLU* 4.4 4.4 - - - +
38H GLY* 3.5 13.3 + - - -
33I GLY* 3.3 32.8 - - - +
36I VAL* 3.5 6.6 - - - +
37I GLU* 4.0 14.7 - - + +
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Residues in contact with ALA 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52G THR* 5.2 1.8 - - + -
31H ALA 2.8 11.3 + - - +
32H ALA 3.4 7.0 - - - +
34H GLN* 1.3 75.0 - - - +
36H VAL* 1.3 66.2 + - - +
37H GLU 3.2 1.6 - - - -
38H GLY* 3.0 3.1 + - - -
39H ILE* 2.9 30.0 + - + +
49H ILE* 4.9 5.2 - - + -
50H ARG 5.8 0.2 - - - +
53H LEU* 3.9 21.8 - - + -
36I VAL* 3.1 32.7 - - + +
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Residues in contact with VAL 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G ALA* 3.9 2.2 - - + +
34G GLN 3.6 1.6 - - - -
35G ALA* 3.1 51.4 - - + +
38G GLY* 5.2 0.2 - - - -
39G ILE* 5.5 0.4 - - + +
49G ILE* 3.7 34.8 - - + +
52G THR* 5.4 8.0 - - - +
53G LEU* 4.9 7.0 - - + +
32H ALA 2.9 11.1 + - - +
33H GLY* 2.9 30.7 - - - +
35H ALA* 1.3 75.2 - - - +
37H GLU* 1.3 61.8 + - - +
39H ILE* 3.7 7.8 + - - +
40H ALA* 3.2 19.6 + - - +
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Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G GLN* 4.0 19.1 - - + +
38G GLY* 4.9 3.6 - - - -
41G ARG* 6.1 3.4 - - - +
33H GLY 3.4 10.3 + - - +
34H GLN* 4.4 4.9 - - - +
35H ALA 3.2 0.4 - - - -
36H VAL* 1.3 79.0 - - - +
38H GLY* 1.3 62.3 + - - +
40H ALA* 2.8 31.2 + - - +
41H ARG* 3.1 13.2 + - - +
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Residues in contact with GLY 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34H GLN 3.5 10.5 + - - -
35H ALA* 3.0 7.0 + - - -
37H GLU* 1.3 78.4 - - - +
39H ILE* 1.3 61.4 + - - +
41H ARG* 3.1 23.4 + - - +
42H GLN* 3.2 11.4 + - - +
36I VAL 5.3 0.2 - - - -
37I GLU* 5.0 4.9 - - - +
40I ALA* 3.6 33.5 - - - +
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Residues in contact with ILE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ALA 5.4 1.1 - - - +
48G LYS* 3.7 34.5 - - + +
49G ILE* 4.8 1.1 - - - +
52G THR* 5.3 6.3 - - + +
35H ALA* 2.9 21.6 + - + +
36H VAL* 3.8 7.4 - - - +
38H GLY* 1.3 72.8 - - - +
40H ALA* 1.3 68.1 + - - +
41H ARG 3.1 0.7 + - - -
42H GLN 3.3 3.8 - - - +
43H PRO* 3.2 28.6 - - + +
45H ALA* 4.3 4.0 - - + +
46H GLU* 3.7 37.9 - - + +
47H GLY 5.4 0.2 - - - +
49H ILE* 2.9 37.9 - - + -
50H ARG* 6.0 1.6 - - + -
36I VAL* 5.6 0.7 - - + +
40I ALA* 5.3 4.0 - - + -
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G GLY* 3.5 40.6 - - - +
39G ILE* 4.5 6.1 - - + +
41G ARG* 5.6 2.7 - - + +
42G GLN* 3.2 26.4 - - - +
45G ALA* 4.5 10.1 - - - -
49G ILE* 6.0 0.9 - - - +
36H VAL 3.2 12.7 + - - +
37H GLU 2.8 13.9 + - - +
39H ILE* 1.3 77.7 - - - +
41H ARG* 1.3 62.0 + - - +
43H PRO* 3.8 5.5 - - - +
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Residues in contact with ARG 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G ARG* 4.5 25.1 - - - +
42G GLN* 4.3 16.8 + - - +
37H GLU* 3.1 11.6 + - - +
38H GLY* 3.1 19.1 + - - +
40H ALA* 1.3 80.9 - - - +
42H GLN* 1.3 86.6 + - - +
43H PRO* 3.2 6.8 - - - +
37I GLU* 6.1 2.6 - - - +
40I ALA* 5.7 2.9 - - + +
41I ARG* 4.6 23.5 - - - +
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Residues in contact with GLN 42 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38H GLY 3.2 5.5 + - - +
39H ILE* 3.3 8.1 - - - +
41H ARG* 1.3 110.1 + - - +
43H PRO* 1.4 60.3 - - - +
44H GLU* 3.3 3.4 - - + +
45H ALA* 3.1 29.2 + - + +
46H GLU 3.7 2.6 + - - -
40I ALA* 3.3 29.9 - - - +
41I ARG* 4.5 11.3 + - - +
43I PRO* 5.6 2.5 - - + -
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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
------------------------------------------------------------
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