Contacts of the helix formed by residues 47 - 59 (chain B) in PDB entry 2WLV
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 47 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B PRO 4.6 1.6 - - - +
2B VAL* 3.7 29.2 - - + -
45B GLY 3.9 0.2 + - - -
46B CYS* 1.4 75.1 - - - +
48B PRO* 1.4 73.3 - - - +
49B TYR 3.4 3.1 + - - -
50B ASP* 2.8 42.7 + - - +
51B ILE* 3.0 15.3 + - - +
109B VAL* 3.5 23.4 - - + +
112B GLN* 3.4 12.8 - - + +
113B ILE* 3.9 9.9 - - + -
116B MET* 4.0 11.2 - - - -
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Residues in contact with PRO 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B THR* 1.4 83.8 - - - +
49B TYR* 1.4 55.3 + - - +
51B ILE* 3.1 2.5 + - + +
52B ASN* 2.8 36.8 + - - -
101B ASP 4.5 0.2 - - - +
102B ILE 3.1 29.4 - - - +
104B GLY 3.9 8.5 - - - +
112B GLN* 3.3 27.4 - - + +
116B MET* 4.6 0.2 - - - -
125B VAL* 3.8 32.3 - - + +
126B GLY* 3.8 10.8 - - - -
129B TYR* 3.8 16.0 - - + -
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B HIS* 3.7 32.5 - + - -
47B THR* 3.2 4.2 - - - +
48B PRO* 1.4 74.6 - - - +
50B ASP* 1.3 64.5 + - - +
52B ASN* 3.2 12.3 + - + +
53B GLN* 3.1 58.3 + - + +
104B GLY* 5.8 0.4 - - - -
109B VAL* 3.9 21.3 - - + +
112B GLN* 2.9 23.5 + - - +
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Residues in contact with ASP 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B PRO* 2.7 34.6 - - - +
11B HIS* 2.7 25.8 - - - -
13B PRO* 4.3 0.3 - - - +
14B LEU* 4.1 12.7 + - + +
46B CYS* 3.6 17.7 - - - -
47B THR* 2.8 32.2 + - - +
49B TYR* 1.3 79.1 - - - +
51B ILE* 1.3 63.8 + - - +
53B GLN* 3.0 13.4 + - - +
54B MET* 3.0 25.9 + - - +
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Residues in contact with ILE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B PHE* 4.1 15.3 - - + -
43B SER* 4.6 3.8 - - - -
46B CYS* 3.9 15.7 - - + -
47B THR 3.0 18.1 + - - +
48B PRO 3.6 5.8 - - - +
50B ASP* 1.3 75.8 - - - +
52B ASN* 1.3 56.6 + - - +
54B MET* 3.1 10.9 + - - +
55B LEU* 2.9 28.3 + - + +
126B GLY 3.6 12.1 - - - +
129B TYR* 3.5 31.6 - - + -
130B ARG* 3.5 33.0 - - + +
133B ILE* 3.8 22.9 - - + -
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Residues in contact with ASN 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PRO 2.8 19.8 + - - +
49B TYR* 3.6 9.2 - - + +
50B ASP 3.2 0.2 - - - -
51B ILE* 1.3 76.8 - - - +
53B GLN* 1.3 59.8 + - - +
55B LEU* 3.2 20.0 + - - +
56B ASN* 3.3 17.1 + - - -
69B ARG* 5.2 3.5 + - - -
103B ALA 2.9 22.2 + - - +
104B GLY* 3.6 18.2 + - - -
105B THR* 5.2 2.2 - - - +
129B TYR* 2.7 24.8 + - - -
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Residues in contact with GLN 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PRO* 5.0 8.4 - - - +
14B LEU* 4.9 17.2 + - + +
19B LEU* 4.2 18.4 - - + +
49B TYR* 3.1 54.9 + - + +
50B ASP* 3.0 15.8 + - - +
52B ASN* 1.3 77.1 - - - +
54B MET* 1.3 61.9 + - - +
56B ASN* 3.1 31.6 + - - +
57B CYS 4.4 0.9 + - - -
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Residues in contact with MET 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B LEU* 3.6 24.5 - - + -
19B LEU* 4.2 7.2 - - + -
22B TRP* 2.8 58.0 + - + +
39B PHE* 3.8 28.9 - - + -
42B LEU* 4.0 28.7 - - + +
43B SER* 3.9 22.4 - - - -
46B CYS* 4.5 2.5 - - - -
50B ASP 3.0 18.0 + - - +
51B ILE* 3.1 12.3 + - - +
53B GLN* 1.3 75.5 - - - +
55B LEU* 1.3 60.8 + - + +
56B ASN 3.3 0.9 + - - -
57B CYS* 3.5 10.6 - - - -
58B VAL* 4.0 0.5 - - - +
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Residues in contact with LEU 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 5.7 3.1 - - + -
39B PHE* 5.7 1.6 - - + -
51B ILE* 2.9 16.1 + - + +
52B ASN* 3.6 17.3 - - - +
53B GLN 3.2 0.6 - - - -
54B MET* 1.3 76.1 - - + +
56B ASN* 1.3 64.4 + - - +
57B CYS 3.3 0.7 - - - -
58B VAL* 3.1 23.7 + - + +
59B GLY* 3.0 19.6 + - - -
65B MET* 4.1 16.3 - - + +
68B ILE* 4.4 20.4 - - + -
69B ARG* 4.7 4.5 - - - +
72B ILE* 4.4 8.3 - - + -
129B TYR* 3.5 25.6 - - + +
133B ILE* 3.9 27.8 - - + -
137B LEU* 6.3 0.4 - - + -
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Residues in contact with ASN 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ASN 3.3 10.6 + - - -
53B GLN* 3.1 28.5 + - - +
55B LEU* 1.3 75.6 - - - +
57B CYS* 1.3 62.4 + - - +
59B GLY* 3.1 14.4 + - - -
60B ASP* 3.9 7.6 + - - +
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Residues in contact with CYS 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B TRP* 3.5 21.8 - - - -
23B VAL* 3.9 33.2 - - + -
26B VAL* 3.8 21.3 - - - -
27B GLN* 4.2 6.9 + - - +
53B GLN 4.4 0.6 + - - -
54B MET 3.5 16.0 + - - -
56B ASN* 1.3 77.4 - - - +
58B VAL* 1.3 64.3 + - - +
60B ASP* 3.1 28.3 + - - +
61B HIS* 3.4 9.4 + - - -
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B TRP* 4.0 22.9 - - + -
26B VAL* 4.3 7.6 - - + -
31B PHE* 4.1 16.8 - - + -
54B MET 4.0 14.4 - - - +
55B LEU* 3.1 19.2 + - + +
57B CYS* 1.3 80.3 - - - +
59B GLY* 1.3 56.9 + - - +
61B HIS* 2.9 37.3 + - - +
65B MET* 3.7 23.6 - - - +
68B ILE* 3.7 27.6 - - + -
137B LEU* 5.6 0.9 - - + -
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B LEU 3.0 11.8 + - - -
56B ASN 3.1 7.8 + - - -
58B VAL* 1.3 77.4 - - - +
60B ASP* 1.3 60.3 + - - +
61B HIS 3.1 1.5 + - - -
62B GLN* 2.8 36.4 + - - +
65B MET* 4.0 8.9 - - - -
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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