Contacts of the helix formed by residues 30 - 42 (chain X) in PDB entry 6L49
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 THR 30 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-183J A 3.2 37.7 + - - +
-182J A 3.3 31.6 - - - +
63W ARG* 3.3 13.6 + - - +
27X GLN 3.8 9.6 - - - +
28X GLY* 3.1 15.8 + - - +
29X ILE* 1.3 73.8 - - - +
31X LYS* 1.3 64.8 + - - +
32X PRO* 3.7 0.7 - - - +
33X ALA* 3.2 11.3 + - - +
34X ILE* 3.1 26.5 + - - +
55X ARG* 3.5 5.6 - - - +
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Residues in contact with LYS 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I C 4.9 12.4 - - - +
178I C 4.9 3.2 + - - -
-182J A 3.7 6.7 + - - +
30X THR* 1.3 76.4 - - - +
32X PRO* 1.3 63.7 - - + +
34X ILE 3.5 1.0 + - - -
35X ARG* 2.9 38.4 + - - +
51X TYR* 3.2 52.7 + - + -
55X ARG* 3.4 13.0 - - - +
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Residues in contact with PRO 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-183J A 3.3 52.5 - - + +
-182J A 3.6 14.6 - - + +
30X THR* 3.7 0.9 - - - +
31X LYS* 1.3 94.6 - - + +
33X ALA* 1.3 56.0 + - - +
35X ARG* 3.4 27.8 + - + +
36X ARG* 2.9 36.0 + - + +
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Residues in contact with ALA 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-183J A 3.7 10.4 + - - +
61W LEU* 4.4 8.0 - - - +
62W ILE* 5.0 10.5 - - + -
63W ARG* 4.3 4.3 - - - +
29X ILE* 4.7 7.6 - - + -
30X THR* 3.2 29.3 + - - +
31X LYS 3.2 1.0 - - - -
32X PRO* 1.3 75.2 - - - +
34X ILE* 1.3 61.2 + - + +
36X ARG* 3.3 19.0 + - - +
37X LEU* 2.9 32.3 + - - +
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Residues in contact with ILE 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W PHE* 4.1 7.6 - - + -
29X ILE* 3.8 16.6 - - + +
30X THR 3.1 16.4 + - - +
33X ALA* 1.3 72.0 - - - +
35X ARG* 1.3 60.7 + - - +
37X LEU* 3.3 10.7 + - + +
38X ALA* 2.9 28.4 + - - +
46X ILE* 6.0 0.2 - - + -
50X ILE* 4.5 2.2 - - + +
51X TYR* 3.5 49.1 - - + +
54X THR* 3.7 33.7 - - + +
55X ARG* 3.6 29.6 - - + +
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Residues in contact with ARG 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178I C 4.6 10.5 + - - +
179I G 4.4 16.0 + - - -
50W GLU* 4.7 17.0 + - - -
31X LYS* 2.9 36.2 + - - +
32X PRO* 3.4 35.8 + - - +
34X ILE* 1.3 76.3 - - - +
36X ARG* 1.3 59.5 + - - +
38X ALA* 3.3 3.1 + - - +
39X ARG* 2.9 40.7 + - + +
46X ILE* 3.7 17.7 - - + +
51X TYR* 3.6 24.7 - - + +
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Residues in contact with ARG 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-184J A 3.8 16.4 + - - +
-183J A 2.4 44.4 + - - -
50W GLU* 6.0 1.8 - - - +
54W TYR* 3.4 33.9 - - + +
61W LEU* 2.7 59.3 + - + +
63W ARG* 4.9 3.4 - - - +
32X PRO* 2.9 23.3 + - - +
33X ALA* 3.3 9.8 + - - +
35X ARG* 1.3 74.0 - - + +
37X LEU* 1.3 60.8 + - - +
39X ARG* 3.3 8.6 + - + +
40X ARG* 2.9 23.7 + - - +
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Residues in contact with LEU 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61W LEU* 3.8 21.5 - - + -
62W ILE* 4.2 17.0 - - + -
97W GLU* 3.9 35.7 - - + +
100W LEU* 3.8 28.5 - - + -
101W VAL* 4.7 5.9 - - + +
104W PHE* 3.6 22.3 - - + -
29X ILE* 5.3 4.3 - - + -
33X ALA 2.9 20.0 + - - +
34X ILE* 3.6 21.8 - - + +
35X ARG 3.3 0.2 - - - -
36X ARG* 1.3 77.1 - - - +
38X ALA* 1.3 56.7 + - - +
40X ARG* 3.4 6.2 + - + +
41X GLY* 2.9 20.8 + - - -
54X THR* 5.0 0.9 - - + -
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Residues in contact with ALA 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104W PHE* 4.0 21.7 - - + -
34X ILE* 2.9 17.6 + - + +
35X ARG 3.3 4.5 + - - +
37X LEU* 1.3 73.7 - - - +
39X ARG* 1.3 61.4 + - - +
41X GLY 3.3 1.2 + - - +
42X GLY 3.0 8.1 + - - -
43X VAL* 2.9 43.5 + - + +
46X ILE* 3.8 26.0 - - + -
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Residues in contact with ARG 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I C 4.5 11.9 + - - -
179I G 4.6 9.1 + - - -
47W ALA* 3.4 39.5 - - - +
50W GLU* 3.7 25.1 + - + +
51W ILE* 3.3 30.9 - - + +
54W TYR* 4.0 19.0 - - + +
55W GLN* 5.6 1.4 + - - +
35X ARG* 2.9 28.9 + - + +
36X ARG* 3.3 10.3 + - + +
38X ALA* 1.3 77.5 - - - +
40X ARG* 1.3 61.1 + - - +
42X GLY* 3.3 4.5 + - - -
43X VAL 2.4 34.1 + - - -
44X LYS 3.4 14.8 + - - -
46X ILE* 3.4 33.9 - - - +
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Residues in contact with ARG 40 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106U GLY* 5.6 6.5 - - - -
107U VAL* 4.0 24.7 - - + +
54W TYR* 3.8 42.0 + - + +
55W GLN* 5.0 16.2 + - + +
57W SER* 4.3 7.3 + - - -
58W THR* 4.6 5.9 + - - +
59W GLU* 2.7 36.7 + - - +
60W LEU* 4.4 2.4 - - - +
61W LEU* 3.6 31.6 - - + +
97W GLU* 3.9 17.6 + - - -
101W VAL* 3.4 23.5 - - + +
105W GLU* 5.3 1.2 - - - +
36X ARG 2.9 16.2 + - - +
37X LEU* 3.7 7.0 - - + +
39X ARG* 1.3 75.0 - - - +
41X GLY* 1.3 61.0 + - - +
42X GLY 3.5 0.5 + - - -
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Residues in contact with GLY 41 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101W VAL* 3.7 16.1 - - - +
104W PHE* 3.8 19.2 - - - +
105W GLU* 3.6 27.2 - - - +
108W ASN* 4.8 2.4 + - - +
37X LEU 2.9 14.7 + - - -
38X ALA 3.3 4.9 + - - -
39X ARG 3.2 0.4 - - - -
40X ARG* 1.3 77.5 - - - +
42X GLY* 1.3 59.0 + - - +
43X VAL* 3.7 1.1 - - - -
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Residues in contact with GLY 42 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110U ASN 5.4 7.9 - - - -
111U ILE* 6.5 0.4 - - - -
112U GLN* 4.7 2.9 - - - +
115U LEU* 3.4 10.2 - - - +
51W ILE* 4.0 17.3 - - - -
55W GLN* 5.6 1.8 - - - -
108W ASN* 2.4 31.1 + - - -
38X ALA 3.0 2.4 + - - -
39X ARG 3.3 8.1 + - - -
40X ARG 3.2 5.0 - - - -
41X GLY* 1.3 79.4 - - - +
43X VAL* 1.3 56.1 + - - +
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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