Contacts of the helix formed by residues 31 - 46 (chain G) in PDB entry 1W4R
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 GLY 31 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G PHE 3.4 3.2 + - - -
30G SER* 1.3 80.8 - - - +
32G LYS* 1.3 65.2 + - - +
33G SER 3.2 2.7 - - - -
34G THR* 3.2 10.7 + - - -
35G GLU* 3.0 19.2 + - - +
149G LEU* 4.0 0.9 - - - -
300G TTP 3.2 11.4 + - - -
38H ARG* 3.3 23.5 - - - -
42H ARG* 4.8 1.3 - - - +
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Residues in contact with LYS 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.9 7.7 - - + +
25G LEU 3.7 10.3 - - - +
26G GLY* 3.5 17.7 - - - +
27G PRO 2.8 23.8 + - - -
28G MET* 4.0 0.4 - - - +
30G SER* 3.3 11.9 - - - +
31G GLY* 1.3 77.0 - - - +
33G SER* 1.3 56.6 + - - +
35G GLU* 3.3 3.3 + - - +
36G LEU* 2.9 28.2 + - - +
122G ALA* 3.7 17.0 - - + +
123G ALA* 3.4 33.0 - - - +
124G LEU* 3.6 3.2 - - - +
149G LEU* 3.8 12.1 - - + -
300G TTP 2.9 62.5 + - - +
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Residues in contact with SER 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G LYS* 1.3 70.6 - - - +
34G THR* 1.3 60.9 + - - +
36G LEU* 3.4 9.3 + - - +
37G MET* 3.0 34.2 + - - +
97G ASP* 2.6 20.7 + - - -
122G ALA* 4.3 0.2 - - - +
300G TTP 2.4 54.2 + - - -
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Residues in contact with THR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G GLY* 3.2 14.9 + - - -
33G SER* 1.3 79.6 - - - +
35G GLU* 1.3 51.9 + - - +
37G MET* 3.2 6.6 + - - +
38G ARG* 2.8 33.1 + - - +
300G TTP 4.2 0.5 + - - -
34H THR* 3.8 24.4 - - + +
38H ARG* 3.7 27.7 - - + +
41H ARG* 4.1 21.0 + - - +
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Residues in contact with GLU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.9 15.3 - - + -
31G GLY 3.0 12.3 + - - +
32G LYS 3.7 7.0 - - - +
34G THR* 1.3 73.4 - - - +
36G LEU* 1.3 64.8 + - - +
38G ARG* 2.9 41.4 + - - +
39G ARG* 2.8 59.1 + - - +
147G VAL* 5.7 0.2 - - + -
149G LEU* 4.1 18.8 - - + -
35H GLU* 3.7 14.8 - - - +
38H ARG* 4.2 6.7 - - - +
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Residues in contact with LEU 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.7 9.5 - - + +
32G LYS 2.9 15.0 + - - +
33G SER* 3.4 10.8 - - - +
34G THR 3.3 0.2 - - - -
35G GLU* 1.3 76.4 - - - +
37G MET* 1.3 64.1 + - - +
39G ARG* 3.2 2.8 + - - +
40G VAL* 2.9 35.7 + - + +
52G VAL* 4.6 9.9 - - + -
95G GLY* 3.8 12.6 - - - -
96G ILE 3.7 27.6 - - - +
97G ASP* 3.9 18.2 - - + +
120G ILE* 3.3 45.3 - - + +
121G VAL 4.5 0.4 - - - +
122G ALA* 4.1 9.9 - - + +
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Residues in contact with MET 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G SER* 3.0 21.4 + - - +
34G THR* 3.7 6.1 - - - +
36G LEU* 1.3 80.5 - - + +
38G ARG* 1.3 66.1 + - - +
40G VAL* 3.9 8.9 - - + +
41G ARG* 2.9 74.3 + - + +
44G GLN* 5.9 0.9 - - - +
52G VAL* 3.9 37.0 - - + -
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Residues in contact with ARG 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G THR 2.8 18.0 + - - +
35G GLU* 2.9 46.4 + - - +
37G MET* 1.3 73.9 - - - +
39G ARG* 1.3 69.8 + - - +
41G ARG* 4.0 6.6 - - - +
42G ARG* 3.2 47.9 + - - +
30H SER 2.8 28.4 + - - +
31H GLY* 3.3 35.4 - - - +
34H THR* 3.9 14.1 - - + -
35H GLU* 4.2 18.2 + - - +
149H LEU* 3.9 25.5 - - - +
150H THR 4.5 1.6 + - - +
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Residues in contact with ARG 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G GLN* 2.9 42.4 + - - +
23G VAL 4.9 1.2 + - - -
24G ILE* 3.7 18.6 - - - +
35G GLU* 2.8 40.3 + - - +
36G LEU 3.6 5.4 - - - +
38G ARG* 1.3 82.6 - - - +
40G VAL* 1.3 67.8 + - - +
42G ARG* 3.3 22.9 + - - +
43G PHE* 3.2 24.1 - - + -
120G ILE* 3.7 20.9 - - + -
145G SER* 4.2 8.4 + - - -
147G VAL* 3.7 35.0 - - - +
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Residues in contact with VAL 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G LEU* 2.9 38.0 + - + +
37G MET* 3.9 13.5 - - + +
39G ARG* 1.3 76.2 - - - +
41G ARG* 1.3 64.1 + - + +
43G PHE* 3.0 13.6 + - - +
44G GLN* 3.0 20.8 + - + +
50G CYS* 3.7 30.0 - - + -
51G LEU 5.5 0.9 - - - +
52G VAL* 4.3 17.0 - - + -
93G VAL* 4.5 6.5 - - + -
95G GLY* 4.3 13.5 - - - +
120G ILE* 4.2 11.4 - - + -
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Residues in contact with ARG 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G MET* 2.9 72.7 + - + +
38G ARG* 4.0 7.0 - - - +
40G VAL* 1.3 73.2 - - + +
42G ARG* 1.3 62.4 + - + +
44G GLN* 3.7 21.9 - - - +
45G ILE* 2.9 27.9 + - - +
34H THR* 4.1 23.4 + - - +
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Residues in contact with ARG 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ARG* 3.2 32.1 + - + +
39G ARG* 3.5 15.7 + - - +
40G VAL 3.2 1.0 - - - -
41G ARG* 1.3 78.0 - - + +
43G PHE* 1.3 73.3 + - - +
45G ILE* 3.3 20.1 - - - +
46G ALA 3.7 2.9 + - - -
29H PHE 3.6 13.2 - - - +
30H SER 3.2 31.6 - - - +
31H GLY* 4.5 1.8 - - - +
150H THR* 3.4 20.1 + - - -
151H ALA* 3.3 7.1 + - - +
152H VAL* 3.3 55.3 + - - +
159H GLU* 5.3 4.0 + - - +
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Residues in contact with PHE 43 (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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20G GLN* 5.5 3.4 - - - -
22G GLN* 5.0 8.3 - - - -
39G ARG* 3.2 24.9 - - + -
40G VAL 3.0 5.9 + - - +
42G ARG* 1.3 88.3 - - - +
44G GLN* 1.3 65.2 + - - +
46G ALA 3.1 10.4 + - - -
47G GLN 3.4 0.2 + - - -
48G TYR* 3.1 52.2 + + + +
50G CYS* 4.3 2.2 - - - -
93G VAL* 3.8 33.7 - - + -
118G THR* 4.2 21.8 - - + -
120G ILE* 4.2 15.9 - - + -
152H VAL* 4.0 18.8 - - + -
157H PHE 5.9 1.3 - - - -
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Residues in contact with GLN 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G MET* 5.9 1.0 - - - +
40G VAL* 3.0 15.9 + - - +
41G ARG* 3.3 25.5 + - - +
43G PHE* 1.3 74.4 - - - +
45G ILE* 1.3 58.8 + - - +
47G GLN* 2.9 23.7 + - - -
48G TYR 3.8 14.8 - - - +
50G CYS* 3.9 19.6 + - - +
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Residues in contact with ILE 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 ARG 2.9 15.8 + - - +
42G ARG* 3.3 18.6 - - - +
44G GLN* 1.3 76.1 - - - +
46G ALA* 1.3 60.0 + - + +
47G GLN* 3.2 10.6 + - - +
29H PHE* 4.2 27.8 - - + +
152H VAL 6.1 0.9 - - - +
154H MET* 3.8 32.1 - - + +
178H ALA* 4.9 10.8 - - + -
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Residues in contact with ALA 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G ARG 3.7 5.1 + - - +
43G PHE 3.1 9.6 + - - +
45G ILE* 1.3 79.5 - - + +
47G GLN* 1.3 71.3 + - - +
48G TYR* 3.3 7.0 + - + -
152H VAL* 3.9 30.5 - - + +
154H MET* 4.3 19.7 - - + -
157H PHE* 3.5 26.5 - - + -
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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
------------------------------------------------------------
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