Contacts of the helix formed by residues 31 - 45 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PHE 3.4 2.0 + - - -
30C SER* 1.3 79.5 - - - +
32C LYS* 1.3 65.3 + - - +
33C SER 3.3 2.7 - - - -
34C THR* 3.2 10.3 + - - -
35C GLU* 3.0 19.1 + - - +
149C LEU* 4.1 0.7 - - - -
300C TTP 3.0 14.4 + - - -
38D ARG* 3.3 23.8 - - - -
42D ARG* 4.8 1.3 - - - +
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Residues in contact with LYS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 4.0 8.0 - - + +
25C LEU 3.8 10.5 - - - +
26C GLY* 3.5 21.1 - - - +
27C PRO 2.8 15.6 + - - -
30C SER* 3.4 10.3 - - - +
31C GLY* 1.3 76.3 - - - +
33C SER* 1.3 58.0 + - - +
35C GLU* 3.3 3.6 + - - +
36C LEU* 2.9 27.2 + - - +
97C ASP* 5.6 0.4 - - - +
122C ALA* 3.8 18.3 - - + +
123C ALA* 3.4 38.4 - - - +
124C LEU* 3.5 3.3 - - - +
149C LEU* 3.9 11.9 - - + -
300C TTP 2.4 64.9 + - - +
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LYS* 1.3 80.3 - - - +
34C THR* 1.3 62.0 + - - +
36C LEU* 3.4 8.5 + - - +
37C MET* 3.0 34.1 + - - +
97C ASP* 3.3 32.7 + - - -
300C TTP 3.1 16.9 + - - -
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Residues in contact with THR 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C GLY* 3.2 14.7 + - - -
33C SER* 1.3 79.7 + - - +
35C GLU* 1.3 60.8 + - - +
37C MET* 3.2 6.0 + - - +
38C ARG* 2.8 27.5 + - - +
34D THR* 3.8 23.9 - - + +
38D ARG* 3.7 28.8 - - + +
41D ARG* 4.0 21.3 + - - +
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Residues in contact with GLU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.8 23.3 - - + -
31C GLY 3.0 12.7 + - - +
32C LYS 3.6 7.2 - - - +
34C THR* 1.3 74.0 - - - +
36C LEU* 1.3 65.1 + - - +
38C ARG* 2.9 41.6 + - - +
39C ARG* 2.9 56.0 + - - +
149C LEU* 4.2 18.4 - - + -
35D GLU* 3.8 13.6 - - - +
38D ARG* 4.2 6.5 - - - +
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Residues in contact with LEU 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ILE* 3.7 9.1 - - + +
32C LYS 2.9 14.2 + - - +
33C SER* 3.4 11.9 - - - +
34C THR 3.3 0.2 - - - -
35C GLU* 1.3 77.6 - - - +
37C MET* 1.3 61.9 + - - +
39C ARG* 3.2 1.9 + - - +
40C VAL* 2.9 46.0 + - + +
52C VAL* 4.4 11.9 - - + -
95C GLY* 3.7 6.5 - - - -
96C ILE 3.9 25.1 - - - +
97C ASP* 4.0 16.8 - - + +
120C ILE* 3.5 36.6 - - + +
122C ALA* 4.1 14.4 - - + +
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Residues in contact with MET 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 3.0 22.7 + - - +
34C THR* 3.2 5.6 + - - +
36C LEU* 1.3 79.7 - - + +
38C ARG* 1.3 65.8 + - - +
40C VAL* 4.4 9.2 - - + +
41C ARG* 2.8 46.7 + - + +
52C VAL* 4.0 39.9 - - + -
34D THR* 5.4 2.2 - - + -
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Residues in contact with ARG 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C THR 2.8 14.1 + - - +
35C GLU* 2.9 46.2 + - - +
37C MET* 1.3 78.5 - - - +
39C ARG* 1.3 71.3 + - - +
41C ARG* 4.0 5.6 - - - +
42C ARG* 3.3 39.4 + - - +
30D SER 2.8 28.5 + - - +
31D GLY* 3.3 36.2 - - - +
34D THR* 3.8 16.7 - - + +
35D GLU* 4.2 17.2 + - - +
149D LEU* 3.8 27.5 - - - +
150D THR 4.3 1.4 + - - +
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Residues in contact with ARG 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 2.9 43.1 + - - +
23C VAL 4.8 1.2 + - - +
24C ILE* 3.7 18.6 - - - +
35C GLU* 2.9 44.1 + - - +
36C LEU 3.6 5.8 - - - +
38C ARG* 1.3 84.2 - - - +
40C VAL* 1.3 65.3 + - - +
42C ARG* 3.3 28.8 + - - +
43C PHE* 3.2 20.7 - - - -
120C ILE* 3.8 20.8 - - + +
145C SER* 4.2 9.4 + - - -
147C VAL* 3.6 35.2 - - - +
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Residues in contact with VAL 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 2.9 39.8 + - + +
37C MET* 4.0 11.4 - - + +
39C ARG* 1.3 77.7 - - - +
41C ARG* 1.3 64.3 + - + +
43C PHE* 3.1 13.2 + - - +
44C GLN* 3.0 21.0 + - + +
50C CYS* 3.8 28.7 - - + -
51C LEU 5.5 0.7 - - - +
52C VAL* 4.2 18.8 - - + -
93C VAL* 4.5 5.6 - - + -
95C GLY* 4.3 13.9 - - - +
120C ILE* 4.2 11.4 - - + -
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Residues in contact with ARG 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C MET* 2.8 37.0 + - + +
38C ARG* 4.0 5.5 - - - +
40C VAL* 1.3 78.8 - - + +
42C ARG* 1.3 62.3 + - - +
44C GLN* 3.7 22.8 - - - +
45C ILE* 3.0 27.0 + - - +
33D SER* 5.9 0.2 + - - -
34D THR* 3.6 24.7 + - - +
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Residues in contact with ARG 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 5.9 1.4 + - - +
38C ARG* 3.3 43.4 + - - +
39C ARG* 3.4 28.1 + - - +
40C VAL 3.2 1.0 - - - -
41C ARG* 1.3 76.0 - - - +
43C PHE* 1.3 77.8 + - - +
45C ILE* 3.3 20.9 - - - +
46C ALA 3.6 3.8 + - - -
29D PHE 3.7 20.6 - - - +
30D SER 3.8 5.2 - - - +
31D GLY* 4.8 0.9 - - - +
150D THR* 2.9 39.5 + - - -
151D ALA* 3.8 13.7 + - - +
152D VAL* 3.7 28.2 + - + +
159D GLU* 4.4 8.7 + - - +
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Residues in contact with PHE 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 5.5 3.8 - - - -
22C GLN* 4.9 8.3 - - - -
39C ARG 3.2 24.9 - - - -
40C VAL* 3.1 6.3 + - - +
42C ARG* 1.3 92.6 - - - +
44C GLN* 1.3 64.0 + - - +
46C ALA* 3.1 12.7 + - - +
47C GLN 3.3 0.2 + - - -
48C TYR* 3.1 50.1 + + + +
50C CYS* 4.2 2.0 - - - -
93C VAL* 3.8 34.5 - - + -
118C THR* 4.1 20.9 - - + -
120C ILE* 4.2 16.2 - - + -
152D VAL* 3.9 18.6 - - + -
157D PHE 5.7 2.5 - - - -
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Residues in contact with GLN 44 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C VAL* 3.0 15.4 + - + +
41C ARG* 3.2 26.8 + - - +
43C PHE* 1.3 77.2 - - - +
45C ILE* 1.3 57.1 + - - +
47C GLN* 2.9 23.9 + - - +
48C TYR 3.9 12.0 + - - +
50C CYS* 3.8 22.7 + - + +
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Residues in contact with ILE 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C ARG 3.0 15.6 + - - +
42C ARG* 3.3 21.3 - - - +
44C GLN* 1.3 76.2 - - - +
46C ALA* 1.3 56.4 + - + +
47C GLN* 3.1 11.0 + - - +
29D PHE* 3.6 41.3 - - + +
152D VAL 6.1 0.9 - - - +
154D MET* 3.8 26.6 - - + +
178D ALA* 4.9 8.3 - - + -
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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