Contacts of the helix formed by residues 30 - 44 (chain G) in PDB entry 4PIW
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 30 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25G LYS* 3.6 19.5 - - - -
27G CYS 3.8 1.5 + - - -
28G GLY 3.2 3.0 - - - -
29G ASP* 1.3 77.6 - - - +
31G GLY* 1.3 65.5 + - - -
33G THR* 3.4 7.5 + - - -
34G ARG* 3.1 26.5 + - - +
237G ASP* 3.3 20.0 - - - -
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Residues in contact with GLY 31 (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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25G LYS* 4.8 5.1 - - - +
30G GLY* 1.3 70.5 - - - +
32G PHE* 1.3 61.8 + - - +
34G ARG* 3.2 18.0 + - - +
35G ARG* 3.3 36.0 + - - +
237G ASP* 3.2 8.5 + - - -
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Residues in contact with PHE 32 (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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16G TYR* 3.6 23.6 - + - -
19G SER* 3.7 20.6 - - - -
20G ALA* 3.6 28.3 - - + -
31G GLY* 1.3 72.0 - - - +
33G THR* 1.3 59.2 + - - +
34G ARG 3.3 0.2 - - - -
35G ARG* 3.4 31.0 - - - +
36G CYS* 2.9 34.0 + - - -
237G ASP* 3.0 19.5 + - - +
240G ALA* 3.9 4.9 - - - +
241G ALA* 3.7 29.8 - - + +
244G TRP* 3.7 35.7 - + + -
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Residues in contact with THR 33 (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 ASP* 3.8 21.9 + - - +
30G GLY 3.4 19.2 + - - -
31G GLY 3.2 0.2 - - - -
32G PHE* 1.3 78.1 - - - +
34G ARG* 1.3 62.4 + - - +
36G CYS 3.6 0.2 + - - -
37G GLN* 3.2 42.2 + - - +
51G LEU* 3.7 24.1 - - + +
207G ARG* 4.0 11.0 - - - +
235G MSE 4.3 7.4 + - + +
237G ASP* 2.8 24.9 + - - -
240G ALA* 3.7 10.9 - - - +
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Residues in contact with ARG 34 (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 ASP* 2.9 46.6 + - - +
30G GLY 3.1 15.7 - - - +
31G GLY* 3.2 8.7 + - - +
33G THR* 1.3 77.6 - - - +
35G ARG* 1.3 59.1 + - + +
37G GLN* 3.3 16.2 + - - +
38G GLN* 2.9 38.6 + - + +
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Residues in contact with ARG 35 (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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31G GLY* 3.3 28.6 + - - +
32G PHE* 3.4 48.0 - - - +
33G THR 3.3 0.2 - - - -
34G ARG* 1.3 74.4 - - + +
36G CYS* 1.3 60.2 + - - +
38G GLN* 3.3 14.5 + - - +
39G TRP 2.9 23.9 + - - -
244G TRP* 3.2 37.2 - - + +
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Residues in contact with CYS 36 (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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32G PHE 2.9 23.3 + - - +
35G ARG* 1.3 75.5 - - - +
37G GLN* 1.3 62.4 + - - +
39G TRP* 3.2 3.3 + - - +
40G LEU* 3.0 31.7 + - + +
51G LEU* 3.8 21.5 - - + -
240G ALA 3.4 23.6 - - - -
243G LEU* 4.1 11.4 - - + -
244G TRP* 3.6 28.0 - - - -
247G LEU* 3.9 17.4 - - + +
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Residues in contact with GLN 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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29G ASP* 5.0 2.8 + - - -
33G THR* 3.2 21.8 + - - +
34G ARG* 3.5 21.9 - - - +
36G CYS* 1.3 77.8 - - - +
38G GLN* 1.3 62.9 + - + +
40G LEU* 3.5 1.0 + - - +
41G GLU* 3.0 37.1 + - - +
48G LYS* 5.4 3.2 - - - +
49G VAL* 3.2 32.4 + - - +
50G LEU* 3.4 9.3 - - - +
51G LEU* 3.1 34.1 + - + -
207G ARG* 3.4 18.8 + - - +
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Residues in contact with GLN 38 (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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34G ARG* 2.9 23.4 + - + +
35G ARG* 3.5 16.5 - - - +
37G GLN* 1.3 75.4 - - + +
39G TRP* 1.3 61.9 + - - +
41G GLU* 4.0 10.9 - - - +
42G GLN* 3.4 31.4 + - + +
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Residues in contact with TRP 39 (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 2.9 13.9 + - - +
36G CYS* 3.2 10.3 + - - +
38G GLN* 1.3 77.6 - - - +
40G LEU* 1.3 82.3 + - + +
42G GLN* 4.2 2.2 - - - +
43G ARG* 3.1 76.7 + - + +
44G PHE* 4.1 9.2 - + - -
158G MSE 4.4 6.3 - - - -
244G TRP* 4.0 23.1 - + + -
247G LEU* 3.5 44.0 + - + -
248G GLU* 5.5 1.2 - - - +
250G ALA* 3.9 20.4 - - + -
251G ASP* 5.8 0.2 - - - -
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Residues in contact with LEU 40 (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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36G CYS* 3.0 21.3 + - + +
37G GLN 4.0 2.9 - - - +
39G TRP* 1.3 97.2 - - + +
41G GLU* 1.3 65.2 + - - +
44G PHE* 3.2 53.6 + - + +
45G GLY 4.0 0.2 + - - -
46G SER* 4.5 1.6 + - - -
49G VAL* 3.8 31.8 - - + +
51G LEU* 4.3 12.3 - - + -
157G VAL* 5.4 2.2 - - + -
175G PHE* 4.6 9.4 - - + -
177G PHE* 4.2 22.9 - - + -
191G ALA* 4.5 3.6 - - + -
193G LEU* 5.5 0.3 - - - +
243G LEU* 5.7 0.4 - - + -
247G LEU* 4.4 15.0 - - + -
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Residues in contact with GLU 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 GLN* 3.0 28.1 + - - +
38G GLN* 4.0 13.6 - - - +
39G TRP 3.3 0.2 - - - -
40G LEU* 1.3 76.7 - - - +
42G GLN* 1.3 69.1 + - + +
45G GLY* 3.2 7.2 + - - -
46G SER 3.2 38.3 + - - +
47G ALA 4.6 2.9 - - - -
48G LYS* 3.5 20.7 - - - +
49G VAL* 2.9 44.7 + - + +
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Residues in contact with GLN 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 GLN* 3.4 20.0 + - + +
39G TRP* 4.3 1.8 - - - +
40G LEU 3.2 0.2 - - - -
41G GLU* 1.3 88.9 + - + +
43G ARG* 1.3 64.5 + - - +
44G PHE 3.3 1.5 + - - -
45G GLY* 3.9 5.5 + - - -
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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
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39G TRP* 3.1 51.2 + - + +
42G GLN* 1.3 78.2 - - - +
44G PHE* 1.3 80.3 + - + +
158G MSE 3.3 20.9 - - - +
165G ALA* 5.3 0.7 - - - +
251G ASP* 2.9 38.2 + - - -
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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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39G TRP* 4.1 10.3 - + - -
40G LEU* 3.2 41.6 + - + +
43G ARG* 1.3 99.0 - - + +
45G GLY* 1.3 62.9 + - - +
46G SER 4.8 0.9 - - - +
157G VAL* 4.2 7.4 - - + -
158G MSE 3.7 45.8 - - - -
164G ARG* 5.7 0.9 - - - +
165G ALA* 3.7 34.4 + - + +
166G LEU 5.2 0.4 - - - +
168G THR* 3.3 22.0 + - - +
175G PHE* 3.7 31.9 - + - -
193G LEU* 5.1 4.7 - - + -
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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
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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