Contacts of the helix formed by residues 52 - 61 (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 ALA 52 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50M ARG* 4.5 7.3 - - + +
51M LEU* 1.4 77.2 - - - +
53M PRO* 1.3 72.7 - - + +
54M GLU* 3.1 10.3 - - + +
55M LEU* 3.3 5.6 + - - +
56M ASN* 3.2 17.8 + - - +
89M LEU 3.6 6.9 + - - -
90M PHE* 3.6 42.8 - - + -
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Residues in contact with PRO 53 (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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50M ARG* 6.2 1.8 - - - +
51M LEU 4.5 1.8 - - - +
52M ALA* 1.3 85.8 - - + +
54M GLU* 1.4 57.3 + - - +
55M LEU 3.4 0.2 - - - -
56M ASN* 3.7 13.5 - - + +
57M GLN* 3.1 26.9 + - - +
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Residues in contact with GLU 54 (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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52M ALA* 3.1 4.1 - - + +
53M PRO* 1.4 79.5 - - - +
55M LEU* 1.4 57.2 + - - +
57M GLN* 3.5 7.2 + - - +
58M ALA* 3.0 25.2 + - + +
90M PHE* 3.8 37.1 - - + +
91M SER* 3.7 25.2 + - - -
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Residues in contact with LEU 55 (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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33M VAL* 6.2 3.6 - - + -
36M ILE* 3.9 21.3 - - + -
51M LEU* 3.8 20.6 - - + -
52M ALA* 3.3 10.8 + - - +
54M GLU* 1.4 75.9 - - - +
56M ASN* 1.4 64.4 + - - +
58M ALA* 3.1 12.7 + - + +
59M ILE* 3.1 26.4 + - + +
71M LEU* 4.2 25.6 - - + -
73M LEU* 4.5 15.5 - - + -
89M LEU* 3.5 39.0 - - + +
90M PHE* 5.2 1.8 - - - +
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Residues in contact with ASN 56 (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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33M VAL* 4.5 14.3 - - - +
52M ALA 3.2 8.5 + - - +
53M PRO* 3.9 18.4 - - + +
54M GLU 3.4 0.2 - - - -
55M LEU* 1.4 76.2 - - - +
57M GLN* 1.4 59.3 + - - +
59M ILE* 3.5 4.1 - - - +
60M TRP* 3.2 55.9 + - - +
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Residues in contact with GLN 57 (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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53M PRO 3.1 19.2 + - - +
54M GLU* 3.6 6.7 - - - +
55M LEU 3.3 0.2 - - - -
56M ASN* 1.4 76.4 - - - +
58M ALA* 1.4 55.9 + - - +
60M TRP* 5.0 3.1 - - - +
61M LYS* 3.0 56.5 + - + +
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Residues in contact with ALA 58 (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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54M GLU* 3.0 16.1 + - + +
55M LEU* 3.1 23.7 + - + +
57M GLN* 1.4 77.1 - - - +
59M ILE* 1.4 55.8 + - - +
61M LYS* 3.3 30.1 - - + +
67M VAL* 5.9 1.0 - - - -
68M GLU* 4.6 14.9 + - - +
71M LEU* 5.8 4.8 - - + +
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Residues in contact with ILE 59 (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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16M LEU* 5.7 1.1 - - + -
20M LEU* 5.2 1.6 - - + -
29M ALA* 4.3 9.4 - - + +
32M ALA* 3.5 32.3 - - + -
33M VAL* 4.1 25.1 - - + -
36M ILE* 4.2 18.2 - - + -
55M LEU* 3.1 17.5 + - + +
56M ASN* 3.5 13.9 - - - +
58M ALA* 1.4 75.5 - - + +
60M TRP* 1.4 76.2 + - + +
61M LYS 3.5 0.7 - - - -
62M ARG 4.9 0.4 - - - -
63M GLY 4.2 0.3 + - - -
64M VAL 4.3 3.3 + - - -
66M GLY 3.4 21.1 - - - +
67M VAL* 3.8 22.2 - - + +
71M LEU* 5.7 6.3 - - + -
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Residues in contact with TRP 60 (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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29M ALA* 3.5 26.0 - - + +
30M PRO* 4.5 13.7 - - + -
33M VAL* 4.8 5.5 - - - +
56M ASN* 3.2 48.0 + - - +
57M GLN* 3.8 4.7 - - - +
59M ILE* 1.4 90.5 - - + +
61M LYS* 1.4 64.0 + - - +
62M ARG 3.5 1.3 - - - -
63M GLY* 3.5 15.0 - - - +
64M VAL* 3.6 28.0 - - + -
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Residues in contact with LYS 61 (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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57M GLN* 3.0 29.2 + - + +
58M ALA* 3.3 34.0 - - - +
60M TRP* 1.4 78.7 - - - +
62M ARG* 1.4 82.1 + - + +
63M GLY* 4.6 0.2 - - - -
68M GLU* 3.5 29.3 + - + +
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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