Contacts of the helix formed by residues 40 - 57 (chain A) in PDB entry 1EXD
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 HIS 40 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A TYR 4.3 4.5 - - - -
39A LEU* 1.3 74.1 - - - +
41A ILE* 1.3 58.8 + - + +
42A GLY* 3.0 25.7 + - - -
43A HIS* 2.6 51.8 + + - +
44A ALA 3.0 7.4 + - - -
260A ARG* 5.2 1.0 + - - -
268A MET* 3.0 47.3 + - + +
270A LYS* 4.5 6.9 + - + +
273A LEU* 3.5 19.7 - - + -
291A PRO* 3.2 19.7 - - + +
292A THR* 3.6 5.8 - - - +
293A ILE* 3.6 8.9 - - - +
998A A 3.7 25.3 + - - -
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Residues in contact with ILE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 1.3 71.0 - - - +
42A GLY* 1.3 62.2 + - - +
44A ALA* 3.0 17.7 + - + +
45A LYS* 3.2 9.2 + - - +
261A LEU* 3.5 13.4 - - + +
263A LEU* 3.9 19.5 - - + -
268A MET* 3.5 24.7 - - - -
291A PRO* 2.8 21.8 + - + +
293A ILE* 4.0 4.3 - - - +
296A LEU* 3.9 20.6 - - + -
306A ILE* 4.3 17.0 - - + -
309A PHE* 3.4 43.1 - - + -
310A CYS* 4.6 0.5 - - - -
327A LEU* 4.6 10.8 - - + -
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Residues in contact with GLY 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS* 3.0 13.8 + - - -
41A ILE* 1.3 81.7 - - - +
43A HIS* 1.3 60.5 + - - +
45A LYS* 3.3 2.4 + - - +
46A SER 3.2 9.4 + - - -
261A LEU* 3.8 11.9 - - - -
268A MET* 4.4 0.9 - - - -
998A A 3.1 47.9 + - - -
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Residues in contact with HIS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.8 13.6 - + + -
39A LEU* 3.5 32.9 - - + +
40A HIS* 2.6 57.3 + + - +
42A GLY* 1.3 70.1 - - - -
44A ALA* 1.3 57.7 + - - -
45A LYS 3.2 0.2 - - - -
46A SER* 3.7 4.5 - - - -
47A ILE* 2.8 36.0 + - + +
270A LYS* 3.6 24.8 + - - -
998A A 2.9 57.9 + + - -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A HIS 3.0 3.8 + - - -
41A ILE* 3.0 14.2 + - + +
43A HIS* 1.3 77.5 - - - +
45A LYS* 1.3 63.5 + - - +
47A ILE* 3.8 0.2 - - - +
48A CYS* 3.0 31.5 + - - -
88A LEU* 4.2 15.5 - - + -
293A ILE* 3.8 17.9 - - + +
306A ILE* 3.6 31.0 - - + -
310A CYS* 3.5 5.2 - - - -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ILE 3.2 11.1 + - - +
42A GLY* 3.5 9.2 - - - +
44A ALA* 1.3 77.7 - - - +
46A SER* 1.3 61.1 + - - +
48A CYS* 3.5 1.9 + - - +
49A LEU* 3.1 23.4 + - + +
258A PHE* 3.5 25.3 - - + -
259A SER* 2.5 34.7 + - - +
260A ARG 4.4 0.4 - - - -
261A LEU* 4.2 15.7 - - + +
310A CYS* 3.5 17.0 - - + +
313A ILE* 4.0 24.7 - - + -
314A GLY 3.9 22.1 + - - +
315A VAL* 4.5 13.9 - - + +
320A ASN* 4.9 5.3 - - - +
998A A 3.9 10.5 - - + -
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Residues in contact with SER 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.7 11.5 - - - -
32A PRO* 5.7 0.2 - - - +
42A GLY 3.2 3.2 + - - -
43A HIS 3.7 6.3 - - - -
45A LYS* 1.3 81.7 - - - +
47A ILE* 1.3 56.6 + - - +
49A LEU* 3.5 4.6 + - - +
50A ASN* 2.9 48.1 + - - +
258A PHE* 4.1 8.4 - - - -
998A A 2.9 51.2 + - - -
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Residues in contact with ILE 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.6 23.8 - - + -
39A LEU* 3.7 27.8 - - + -
43A HIS 2.8 30.8 + - - +
44A ALA 3.8 4.3 - - - +
45A LYS 3.3 0.2 - - - -
46A SER* 1.3 70.4 - - - +
48A CYS* 1.3 61.0 + - - +
51A PHE* 2.9 52.8 + - + +
85A VAL* 3.9 15.3 - - + +
88A LEU* 3.7 21.1 - - + -
90A PHE* 3.4 26.0 - - + -
293A ILE* 5.7 1.3 - - + -
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Residues in contact with CYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 5.2 1.6 + - - -
44A ALA* 3.0 27.2 + - - +
45A LYS 3.8 3.4 - - - +
47A ILE* 1.3 76.4 - - - +
49A LEU* 1.3 58.6 - - - +
52A GLY* 2.8 31.4 + - - -
53A ILE 3.9 0.2 + - - -
88A LEU* 5.2 2.2 - - - -
90A PHE* 4.0 28.9 - - + -
306A ILE* 5.4 0.7 - - - -
307A ARG* 4.1 17.9 - - - +
310A CYS* 3.7 27.6 - - + -
311A LYS 5.7 0.2 - - - +
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASN* 4.3 17.7 - - - +
11A ILE* 3.8 11.7 - - + -
12A ARG* 5.4 2.5 - - - +
45A LYS 3.1 15.8 + - - +
46A SER* 3.7 5.4 - - - +
48A CYS* 1.3 78.3 - - - +
50A ASN* 1.3 57.8 + - - +
53A ILE* 3.0 60.4 + - + +
228A LEU* 3.4 22.9 - - + -
258A PHE* 3.6 37.7 - - + -
315A VAL* 4.1 16.2 - - + -
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Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 2.9 28.8 + - - +
30A ARG* 3.1 29.3 + - - +
31A PHE* 4.6 6.8 - - + +
32A PRO* 5.5 0.6 - - - +
46A SER* 2.9 37.5 + - - +
47A ILE 4.5 0.4 - - - +
49A LEU* 1.3 84.3 - - - +
51A PHE* 1.3 61.1 + - - +
53A ILE* 3.9 1.5 - - - +
54A ALA* 3.3 12.1 + - - +
61A CYS* 3.7 11.2 - - - -
228A LEU* 3.3 42.1 + - - +
258A PHE* 5.3 0.4 - - - -
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.5 28.5 - + + -
47A ILE* 2.9 48.5 + - + +
50A ASN* 1.3 71.5 - - + +
52A GLY* 1.3 64.2 + - - +
54A ALA* 3.4 2.8 + - - +
55A GLN* 3.0 25.6 + - - +
61A CYS* 3.8 24.7 - - + -
62A ASN 4.3 3.8 - - - -
63A LEU* 4.6 5.6 - - + -
85A VAL* 3.6 22.2 - - + -
90A PHE* 3.4 27.5 - - + -
91A HIS 3.5 16.4 - - - -
92A TRP* 3.6 36.1 - - + -
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Residues in contact with GLY 52 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ARG* 3.9 2.5 - - - -
48A CYS 2.8 24.2 + - - -
51A PHE* 1.3 70.5 - - - +
53A ILE* 1.3 62.7 + - - +
55A GLN* 3.0 18.1 + - - +
56A ASP* 2.7 37.6 + - - +
90A PHE* 4.3 5.9 - - - -
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.1 7.0 - - + -
12A ARG* 3.6 34.1 - - + +
15A ILE* 3.5 35.9 - - + -
27A VAL* 4.0 14.1 - - + -
29A THR* 4.0 9.9 - - + -
49A LEU* 3.0 47.1 + - + +
50A ASN 3.9 2.5 - - - +
52A GLY* 1.3 74.1 - - - +
54A ALA* 1.3 65.5 + - - +
56A ASP* 3.2 0.8 + - - -
57A TYR* 2.9 33.2 + - + -
228A LEU* 4.0 14.8 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A VAL* 4.0 12.6 - - + -
29A THR* 3.7 3.6 - - - +
50A ASN 3.3 12.4 + - - +
51A PHE 3.6 8.1 - - - +
52A GLY 3.2 0.6 - - - -
53A ILE* 1.3 80.5 - - - +
55A GLN* 1.3 63.9 + - - +
57A TYR 3.2 0.7 + - - -
58A LYS 3.0 4.3 + - - -
59A GLY 2.7 27.7 + - - +
60A GLN* 3.5 37.5 - - - +
61A CYS* 3.7 5.6 - - + +
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Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A PHE 3.0 16.8 + - - +
52A GLY* 3.1 26.8 - - - +
54A ALA* 1.3 72.1 - - - +
56A ASP* 1.3 75.0 + - - +
58A LYS* 3.0 27.8 + - - +
59A GLY 4.9 2.7 - - - +
90A PHE* 4.5 19.3 - - - -
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Residues in contact with ASP 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 2.7 42.4 + - - +
52A GLY* 2.7 29.8 + - - +
53A ILE 3.7 1.8 - - - +
55A GLN* 1.3 83.1 + - - +
57A TYR* 1.3 63.3 + - + +
58A LYS* 3.1 19.0 + - - +
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Residues in contact with TYR 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 3.2 49.2 + - + +
15A ILE* 3.4 19.7 - - + -
16A ASP* 2.8 30.0 + - - -
19A LEU* 3.7 22.8 - - + +
26A THR* 5.7 1.6 - - - -
27A VAL* 3.9 22.6 + - + +
53A ILE* 2.9 41.5 + - + +
56A ASP* 1.3 78.6 - - + +
58A LYS* 1.3 70.0 + - - +
59A GLY* 2.9 3.4 + - - -
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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