Contacts of the helix formed by residues 22 - 37 (chain V) in PDB entry 4IL6
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 22 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8V LEU* 4.1 2.6 - - - +
20V THR 5.1 2.9 - - - +
21V LEU* 1.3 78.6 - - - +
23V GLU* 1.3 59.1 + - - +
24V LYS* 3.5 11.1 + - - +
25V GLN* 3.0 37.6 + - - +
26V TYR* 3.0 25.6 + - - +
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Residues in contact with GLU 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A ALA 5.6 0.5 - - - +
3V LEU* 4.0 37.8 - - + +
8V LEU* 4.0 10.6 - - + +
22V THR* 1.3 72.6 - - - +
24V LYS* 1.3 56.8 + - - +
26V TYR* 3.3 8.1 + - - +
27V LEU* 3.0 39.9 + - + +
207V GOL 2.9 30.4 + - - -
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Residues in contact with LYS 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 3.2 10.2 - - - +
23V GLU* 1.3 75.9 - - - +
25V GLN* 1.3 60.9 + - + +
27V LEU* 3.4 14.1 + - + +
28V GLU* 2.9 57.1 + - + +
110V LYS* 5.5 5.8 - - - +
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Residues in contact with GLN 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19V ILE* 6.0 2.7 - - - +
20V THR 4.4 2.3 - - - +
21V LEU* 3.3 33.7 - - + +
22V THR* 3.0 43.8 + - - +
24V LYS* 1.3 75.3 - - + +
26V TYR* 1.3 61.0 + - - +
28V GLU* 3.7 6.1 - - - +
29V GLY* 2.8 27.2 + - - -
110V LYS* 5.7 6.4 + - + +
113V VAL* 4.1 17.0 - - - +
114V ALA* 4.0 16.0 - - + +
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Residues in contact with TYR 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A LYS 5.1 1.2 + - - -
311A GLY* 5.5 2.3 - - - -
45F ARG* 4.3 20.0 + - - -
3V LEU* 3.8 20.4 - - + -
8V LEU* 3.8 30.5 - - + -
21V LEU* 5.1 3.3 - - - +
22V THR 3.0 8.4 + - - +
23V GLU* 3.3 11.8 + - - +
25V GLN* 1.3 75.9 - - - +
27V LEU* 1.3 72.9 + - + +
29V GLY* 3.2 2.8 + - - -
30V LYS* 3.0 38.5 + - + +
117V GLY 6.1 0.9 - - - -
118V HIS* 4.3 14.9 - + - +
121V VAL* 3.7 24.7 - - + -
122V GLU* 2.9 35.3 + - - -
125V ILE* 3.5 15.2 - - + +
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Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ARG* 5.7 3.1 - - - +
40J LEU* 5.6 6.1 - - - +
23V GLU* 3.0 25.5 + - + +
24V LYS* 3.7 17.3 - - + +
26V TYR* 1.3 86.8 - - + +
28V GLU* 1.3 60.2 + - + +
30V LYS* 3.3 9.2 + - + +
31V ARG* 2.9 30.2 + - - +
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Residues in contact with GLU 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V LYS* 2.9 50.4 + - + +
25V GLN* 3.7 6.3 - - - +
27V LEU* 1.3 74.9 - - - +
29V GLY* 1.3 55.8 + - - +
31V ARG* 2.7 48.8 + - - +
32V LEU* 2.8 48.3 + - + +
110V LYS* 4.6 13.8 + - - +
111V ASP* 4.5 4.3 - - - +
114V ALA* 4.2 10.5 - - + -
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Residues in contact with GLY 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25V GLN 2.8 17.6 + - - -
26V TYR* 3.2 2.7 + - - -
28V GLU* 1.3 73.1 - - - +
30V LYS* 1.3 55.8 + - - +
32V LEU* 3.9 1.1 - - - +
33V PHE* 2.8 32.6 + - - +
114V ALA* 3.3 33.1 - - - +
115V ILE* 4.1 2.4 - - - -
118V HIS* 3.7 11.8 - - - +
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Residues in contact with LYS 30 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A ILE* 5.7 3.8 - - - +
45F ARG* 4.2 3.8 - - - +
39J SER 3.9 7.7 + - - -
40J LEU* 2.9 45.4 + - + +
26V TYR* 3.0 36.6 + - + +
27V LEU* 3.7 11.7 - - + +
29V GLY* 1.3 74.7 - - - +
31V ARG* 1.3 63.5 + - - +
33V PHE* 3.8 1.6 - - - +
34V GLN* 3.0 49.2 + - + +
118V HIS* 3.7 29.4 - - + +
122V GLU* 4.8 5.7 + - - -
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Residues in contact with ARG 31 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27V LEU 2.9 16.9 + - - +
28V GLU* 2.7 44.6 + - - +
30V LYS* 1.3 78.5 - - - +
32V LEU* 1.3 77.6 + - - +
34V GLN* 3.4 8.4 + - - +
35V TYR* 2.9 29.9 + - + +
111V ASP* 4.8 2.6 + - - -
205V DMS 2.7 38.2 + - - +
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Residues in contact with LEU 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28V GLU* 2.8 38.2 + - - +
29V GLY 4.1 0.2 - - - +
31V ARG* 1.3 94.4 - - - +
33V PHE* 1.3 60.3 + - - +
35V TYR* 3.1 6.4 + - + +
36V ALA* 2.9 32.7 + - - +
107V LEU* 3.8 11.2 - - + -
111V ASP* 3.5 41.1 - - + +
114V ALA* 4.0 6.3 - - + -
115V ILE* 3.6 20.1 - - + +
205V DMS 3.7 28.7 - - + +
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Residues in contact with PHE 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C SER* 6.0 1.6 - - - -
29V GLY 2.8 19.5 + - - +
30V LYS 3.8 2.5 - - - +
32V LEU* 1.3 75.5 - - - +
34V GLN* 1.3 62.7 + - + +
37V CYS* 2.8 54.2 + - + +
38V ALA* 2.8 26.6 + - + -
41V HIS* 3.4 35.0 - + + -
42V VAL* 4.6 3.4 - - - -
43V GLY 4.9 0.9 - - - -
54V LEU* 3.9 18.8 - - + -
115V ILE* 4.0 10.2 - - + +
118V HIS* 3.5 28.3 - + + +
119V ILE* 4.1 17.9 - - + -
130V TRP* 3.9 19.5 - + - -
201V HEM 5.5 0.2 - - + -
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Residues in contact with GLN 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416C SER* 3.1 35.5 + - - +
417C VAL* 6.0 1.2 - - - +
418C ASN* 5.7 0.4 - - - +
517C DGD 3.3 23.2 + - - -
40J LEU* 3.5 23.4 - - - +
30V LYS* 3.0 35.6 + - + +
31V ARG* 3.6 7.5 - - - +
33V PHE* 1.3 80.7 - - + +
35V TYR* 1.3 64.6 + - - +
38V ALA* 3.6 22.6 + - + +
39V SER 5.0 1.4 + - - -
103V LYS* 5.1 0.7 + - - -
118V HIS* 6.3 0.2 - - + -
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Residues in contact with TYR 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ILE* 5.1 3.4 - - + -
78C GLU* 3.8 9.7 + - - +
79C LYS* 3.9 37.7 - - + +
83C GLU* 4.7 0.3 - - - +
31V ARG* 2.9 21.5 + - + +
32V LEU* 3.1 10.0 + - + +
34V GLN* 1.3 78.5 - - - +
36V ALA* 1.3 61.8 + - + +
103V LYS* 2.7 76.5 + - + +
106V ASN* 3.1 20.3 + - - -
107V LEU* 4.3 5.4 - - + -
205V DMS 3.4 43.7 - - + -
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Residues in contact with ALA 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32V LEU 2.9 10.8 + - - +
35V TYR* 1.3 94.5 - - + +
37V CYS* 1.3 60.2 + - - +
39V SER* 5.1 1.3 + - - -
93V PRO* 5.0 3.1 - - - +
103V LYS* 4.2 16.9 + - + +
104V MET* 4.4 6.6 - - - +
107V LEU* 4.2 14.1 - - + -
115V ILE* 4.9 0.9 - - + -
201V HEM 3.6 40.6 - - + +
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Residues in contact with CYS 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V PHE* 2.8 47.5 + - + +
35V TYR 3.8 0.2 - - - -
36V ALA* 1.3 78.3 - - - +
38V ALA* 1.3 60.1 + - - +
39V SER* 3.3 4.7 - - - -
40V CYS* 3.2 6.4 + - - +
41V HIS* 2.9 28.0 + - + +
115V ILE* 4.1 6.3 - - - -
201V HEM 2.1 66.1 - - + +
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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