Contacts of the helix formed by residues 28 - 45 (chain M) in PDB entry 2WW9
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 ARG 28 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M LEU* 3.4 41.6 + - + +
21M HIS* 3.3 24.7 + - - +
23M VAL* 2.9 39.3 + - + -
24M SER* 3.7 26.8 + - - +
27M LYS* 1.4 73.7 - - - +
29M ALA* 1.4 60.3 + - - +
30M PRO 3.6 0.2 - - - -
31M ARG* 3.3 7.6 + - - +
32M ALA* 3.0 28.4 + - + +
64M VAL* 3.2 32.3 + - + +
65M LYS* 2.9 33.7 + - - +
67M VAL* 5.2 4.3 - - + +
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Residues in contact with ALA 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M ARG* 1.4 78.2 - - - +
30M PRO* 1.3 69.6 - - + +
32M ALA* 3.3 7.6 + - - +
33M VAL* 3.1 27.7 + - - +
59M ILE* 4.3 11.4 - - + +
60M TRP* 3.5 38.4 - - + +
64M VAL* 4.0 19.6 - - + +
67M VAL* 6.4 0.9 - - + -
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Residues in contact with PRO 30 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27M LYS* 4.4 28.7 - - + +
28M ARG 3.8 1.3 - - - -
29M ALA* 1.3 94.1 - - + +
31M ARG* 1.4 61.0 + - - +
33M VAL* 3.8 7.8 + - + +
34M LYS* 3.5 19.2 + - - +
60M TRP* 4.5 13.5 - - + +
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Residues in contact with ARG 31 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19M ARG* 5.5 9.9 - - - +
20M LEU* 5.8 3.6 - - + -
23M VAL* 5.1 16.8 - - + -
27M LYS 4.4 9.0 - - - +
28M ARG* 3.3 8.9 + - - +
30M PRO* 1.4 78.4 - - - +
32M ALA* 1.4 59.2 + - - +
34M LYS* 3.3 14.1 + - - +
35M GLU* 2.9 58.2 + - + +
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Residues in contact with ALA 32 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 5.5 0.9 - - + +
20M LEU* 3.8 35.0 - - + +
28M ARG* 3.0 19.3 + - + +
29M ALA* 3.5 7.6 - - - +
31M ARG* 1.4 74.5 - - - +
33M VAL* 1.4 59.6 + - - +
35M GLU* 3.4 5.3 + - - +
36M ILE* 3.0 33.7 + - + +
59M ILE* 3.5 20.6 - - + -
67M VAL* 5.7 0.7 - - + -
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Residues in contact with VAL 33 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29M ALA 3.1 17.7 + - - +
30M PRO* 4.0 8.3 - - + +
31M ARG 3.4 0.2 - - - -
32M ALA* 1.4 73.7 - - - +
34M LYS* 1.4 58.3 + - - +
36M ILE* 3.4 10.2 + - + +
37M LYS* 3.0 26.0 + - - +
51M LEU* 3.8 27.2 - - + +
55M LEU* 6.2 3.6 - - + -
56M ASN* 4.5 13.5 - - - +
59M ILE* 4.1 28.3 - - + -
60M TRP* 4.8 4.7 - - - +
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Residues in contact with LYS 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30M PRO 3.5 11.4 + - - +
31M ARG* 3.3 18.9 + - - +
33M VAL* 1.4 78.3 - - - +
35M GLU* 1.4 60.3 + - - +
37M LYS* 3.2 12.4 + - + +
38M LYS* 3.1 30.1 + - + +
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Residues in contact with GLU 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M LEU* 5.5 3.8 - - + -
19M ARG* 4.9 15.3 - - + +
20M LEU* 5.1 10.1 - - + -
31M ARG* 2.9 53.8 + - + +
32M ALA* 3.5 12.6 - - - +
33M VAL 3.3 0.4 - - - -
34M LYS* 1.4 73.9 - - - +
36M ILE* 1.4 58.8 + - + +
38M LYS* 3.4 22.8 + - - +
39M PHE* 3.0 62.3 + - + -
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Residues in contact with ILE 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 4.1 22.4 - - + +
16M LEU* 4.5 20.2 - - + -
32M ALA* 3.0 21.4 + - + +
33M VAL* 3.8 7.9 - - + +
34M LYS 3.4 0.2 - - - -
35M GLU* 1.4 74.7 - - - +
37M LYS* 1.4 57.5 + - - +
39M PHE* 3.9 6.1 - - - +
40M ALA* 3.0 29.7 + - + +
51M LEU* 4.4 3.1 - - + -
55M LEU* 3.9 31.9 - - + -
59M ILE* 4.2 17.7 - - + -
71M LEU* 4.1 25.8 - - + -
73M LEU* 4.2 6.5 - - + -
89M LEU* 4.4 7.0 - - + -
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Residues in contact with LYS 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M VAL 3.0 14.1 + - - +
34M LYS* 3.2 16.7 + - + +
36M ILE* 1.4 78.0 - - - +
38M LYS* 1.4 56.6 + - - +
41M LYS* 3.2 19.4 + - - +
47M ASP 6.1 0.2 - - - -
48M ASP* 3.4 18.6 + - - +
49M VAL* 2.9 53.9 + - + +
50M ARG 4.6 2.4 + - - -
51M LEU* 3.9 29.5 - - + +
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Residues in contact with LYS 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M LYS* 3.1 23.5 + - + +
35M GLU* 3.4 43.0 + - - +
37M LYS* 1.4 73.6 - - + +
39M PHE* 1.4 95.8 + - - +
40M ALA 3.4 0.2 - - - -
41M LYS* 3.6 16.7 - - + +
42M LEU* 3.3 38.0 + - - +
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Residues in contact with PHE 39 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 4.1 29.4 - - + -
15M ASN 4.9 9.9 - - - -
16M LEU* 5.3 4.7 - - + -
18M LYS* 6.0 6.3 - - + -
19M ARG* 6.5 0.4 - - - -
35M GLU* 3.0 49.6 + - + +
36M ILE* 3.4 4.9 + - - +
38M LYS* 1.4 91.8 - - - +
40M ALA* 1.4 59.1 + - - +
42M LEU* 3.2 14.0 + - + +
43M HIS* 2.9 48.6 + + + +
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Residues in contact with ALA 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 5.4 6.0 - - + +
36M ILE* 3.0 20.3 + - + +
37M LYS 4.1 0.2 - - - +
39M PHE* 1.4 72.9 - - - +
41M LYS* 1.4 59.1 + - - +
43M HIS* 4.0 7.2 - - - +
44M MET* 3.1 32.2 + - - +
46M THR* 4.1 1.9 - - - +
49M VAL* 3.8 25.4 - - + -
75M ILE* 4.2 7.4 - - + +
89M LEU* 4.0 18.8 - - + -
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Residues in contact with LYS 41 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37M LYS 3.2 18.2 + - - +
38M LYS* 3.6 17.7 - - + +
39M PHE 3.2 0.2 - - - -
40M ALA* 1.4 77.0 - - - +
42M LEU* 1.4 58.8 + - + +
45M GLY* 3.0 23.6 + - - -
46M THR* 3.2 33.9 + - - +
47M ASP* 3.5 25.8 - - - +
49M VAL* 3.9 7.0 - - + -
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Residues in contact with LEU 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M LYS* 3.3 33.0 + - + +
39M PHE* 3.2 16.7 + - + +
41M LYS* 1.4 78.4 - - + +
43M HIS* 1.4 66.7 + - + +
45M GLY* 3.7 7.0 + - - -
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Residues in contact with HIS 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ARG* 3.2 20.2 + - - -
12M TYR* 3.8 52.8 + + + +
13M THR 5.9 1.2 + - - -
14M ILE* 5.8 9.5 - - + +
39M PHE* 2.9 47.2 + + + +
40M ALA* 4.3 6.3 - - - +
42M LEU* 1.4 79.9 - - + +
44M MET* 1.4 60.9 + - - +
45M GLY 3.7 0.2 + - - -
75M ILE* 5.4 4.0 - - + -
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Residues in contact with MET 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ARG* 3.6 21.1 + - - +
40M ALA 3.1 17.8 + - - +
43M HIS* 1.4 79.5 - - - +
45M GLY* 1.4 62.2 + - - +
46M THR* 3.5 25.1 - - + +
75M ILE* 3.7 28.5 - - + -
76M SER 3.4 22.0 - - - +
77M ARG* 3.8 9.9 - - - -
78M LYS* 3.6 29.8 - - + +
86M LYS 3.9 1.8 - - - +
87M ASN* 3.5 23.8 - - + +
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Residues in contact with GLY 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41M LYS 3.0 10.7 + - - -
42M LEU 3.7 6.5 + - - -
43M HIS 3.4 3.2 - - - -
44M MET* 1.4 78.8 - - - +
46M THR* 1.4 58.7 + - - +
78M LYS* 4.3 10.0 - - - +
81M GLU* 5.7 0.7 - - - +
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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
------------------------------------------------------------
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