Contacts of the helix formed by residues 36 - 51 (chain G) in PDB entry 3WTV
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 PRO 36 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34G ASP 4.5 0.9 - - - +
35G ARG* 1.3 111.1 - - + +
37G HIS* 1.3 67.0 + - - +
38G GLU* 4.1 19.5 - - + +
39G GLU* 2.9 19.6 + - + +
40G ARG* 3.1 8.1 + - - +
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Residues in contact with HIS 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35G ARG 3.5 2.5 + - - -
36G PRO* 1.3 72.7 - - - +
38G GLU* 1.3 61.4 + - - +
40G ARG* 3.8 17.1 + - - +
41G GLN* 3.1 45.1 + - + +
117G HIS 2.7 25.9 + - - -
118G ARG* 4.4 9.0 - - - -
119G LEU* 4.1 18.4 - - + +
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Residues in contact with GLU 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G PRO* 2.9 14.7 + - + +
37G HIS* 1.3 79.4 - - - +
39G GLU* 1.3 86.0 + - - +
41G GLN* 3.4 15.0 + - - +
42G THR* 3.2 32.4 + - + +
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Residues in contact with GLU 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G PHE* 4.6 0.3 - - - -
35G ARG* 2.7 55.3 + - + +
36G PRO* 2.9 12.4 + - + +
38G GLU* 1.3 92.1 + - - +
40G ARG* 1.3 65.4 + - - +
42G THR* 2.7 25.6 + - - +
43G ARG* 2.9 48.0 + - + +
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Residues in contact with ARG 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113F TYR* 5.8 0.4 + - - -
28G LYS* 5.8 4.2 - - - +
29G TYR* 2.8 58.6 + - + +
30G THR* 3.8 3.2 - - - +
31G GLY 2.9 21.7 + - - +
32G PHE* 3.1 23.7 + - + +
33G ARG* 3.9 17.7 - - - +
35G ARG* 3.6 23.3 - - + +
36G PRO 3.1 6.9 + - - +
37G HIS* 3.8 19.4 + - - +
39G GLU* 1.3 75.8 - - - +
41G GLN* 1.3 57.7 + - - +
43G ARG* 4.5 7.0 - - - +
44G PHE* 2.9 32.2 + - - +
119G LEU* 3.7 27.5 - - + +
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Residues in contact with GLN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37G HIS* 3.1 34.7 + - - +
38G GLU* 3.6 13.3 - - - +
39G GLU 3.1 0.2 - - - -
40G ARG* 1.3 75.1 - - - +
42G THR* 1.3 64.9 + - + +
44G PHE* 4.0 2.4 - - - +
45G GLN* 3.2 23.7 + - - +
116G LEU* 3.5 21.3 - - - +
117G HIS* 2.8 45.3 + - - +
119G LEU* 3.6 20.1 - - + +
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Residues in contact with THR 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38G GLU* 3.2 25.1 + - + +
39G GLU* 2.7 24.3 + - - +
41G GLN* 1.3 76.2 - - + +
43G ARG* 1.3 65.3 + - - +
45G GLN* 3.3 4.8 + - - +
46G ASN* 2.7 42.2 + - - +
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Residues in contact with ARG 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G TYR* 4.2 9.4 - - - +
32G PHE* 3.4 55.1 - - + -
39G GLU* 2.9 50.1 + - + +
40G ARG* 3.9 4.0 - - - +
42G THR* 1.3 85.0 + - - +
44G PHE* 1.3 65.0 + - - +
45G GLN 3.1 0.2 + - - -
46G ASN* 3.9 5.5 - - - +
47G ALA* 2.9 28.8 + - + +
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Residues in contact with PHE 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TYR* 3.2 46.6 + + + -
40G ARG 2.9 19.7 + - - +
41G GLN 4.0 3.4 - - - +
43G ARG* 1.3 75.5 - - - +
45G GLN* 1.3 61.6 + - - +
47G ALA* 3.7 4.3 - - - +
48G CYS* 3.0 48.6 + - + -
53G SER* 3.3 20.4 + - - -
95G VAL* 4.7 5.6 - - + -
97G LEU* 4.3 2.9 - - + -
114G ILE* 3.5 51.4 - - + -
116G LEU* 4.2 21.3 - - + -
119G LEU* 4.4 13.2 - - + -
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Residues in contact with GLN 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G GLN 3.2 14.8 + - - +
42G THR* 3.8 4.5 - - - +
43G ARG 3.1 0.6 - - - -
44G PHE* 1.3 80.3 - - - +
46G ASN* 1.3 71.2 + - - +
47G ALA 2.9 1.1 - - - -
48G CYS* 2.7 18.4 + - + +
49G ARG* 2.9 55.7 + - + +
88G LEU* 5.2 4.9 - - + -
116G LEU* 3.2 38.9 - - + +
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Residues in contact with ASN 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G THR* 2.7 34.1 + - - +
43G ARG* 4.0 5.2 - - - +
45G GLN* 1.3 79.8 + - - +
47G ALA* 1.3 59.4 + - - +
49G ARG* 3.4 20.0 + - - +
50G ASP* 2.9 33.6 + - - +
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Residues in contact with ALA 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TYR* 5.3 4.3 - - + +
43G ARG 2.9 20.3 + - - +
44G PHE* 3.7 6.7 - - - +
46G ASN* 1.3 75.5 - - - +
48G CYS* 1.3 59.9 + - - +
50G ASP* 3.0 22.4 + - - +
51G GLY 3.0 8.0 + - - -
52G ARG* 2.9 48.2 + - - +
53G SER* 5.1 3.6 - - - -
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Residues in contact with CYS 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44G PHE* 3.0 53.6 + - + +
45G GLN* 2.7 13.9 + - - +
47G ALA* 1.3 68.2 - - - +
49G ARG* 1.3 59.9 + - + +
50G ASP 3.0 5.4 - - - -
51G GLY* 3.0 18.1 + - - +
52G ARG 3.6 4.3 - - - -
53G SER* 4.2 4.5 - - - -
68G PHE* 4.2 8.6 - - - -
86G VAL* 3.5 29.2 - - + +
88G LEU* 5.8 2.9 - - + -
95G VAL* 4.8 6.1 - - + -
97G LEU* 3.9 23.6 - - + -
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Residues in contact with ARG 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G GLN* 2.9 54.9 + - + +
46G ASN* 3.6 21.9 + - - +
48G CYS* 1.3 77.1 - - + +
50G ASP* 1.3 62.8 + - - +
51G GLY 3.4 0.2 - - - -
81G PRO* 4.3 18.7 - - - +
86G VAL* 4.9 8.6 - - + +
88G LEU* 3.1 40.2 - - + +
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Residues in contact with ASP 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46G ASN* 2.9 17.8 - - - +
47G ALA* 3.0 13.2 + - - +
49G ARG* 1.3 85.4 - - - +
51G GLY* 1.3 57.1 + - - +
52G ARG* 3.6 27.7 + - - +
69G PHE* 3.2 18.8 - - - -
81G PRO* 4.6 5.4 - - - +
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Residues in contact with GLY 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G CYS 3.0 13.5 + - - -
49G ARG 3.4 0.6 - - - -
50G ASP* 1.3 79.6 - - - +
52G ARG* 1.3 58.9 + - - +
67G GLN* 3.3 5.4 + - - -
68G PHE* 2.7 44.9 + - - -
69G PHE* 3.6 21.7 - - - -
81G PRO* 6.0 0.9 - - - -
82G SER 6.3 0.2 - - - -
86G VAL* 5.7 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
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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