Contacts of the helix formed by residues 38 - 56 (chain A) in PDB entry 2AIA
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 SER 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PRO 3.8 1.0 + - - -
37A LEU* 1.3 76.8 - - - +
39A ASP* 1.3 63.3 + - - +
40A GLN* 3.5 9.3 + - - +
41A GLU* 3.0 42.5 + - - +
42A ILE* 3.2 13.1 + - - +
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Residues in contact with ASP 39 (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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37A LEU 4.0 0.7 + - - +
38A SER* 1.3 73.4 - - - +
40A GLN* 1.3 59.7 + - + +
42A ILE* 3.1 14.9 + - - +
43A ILE* 2.9 44.6 + - + +
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Residues in contact with GLN 40 (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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3A ILE* 4.0 29.8 + - + +
4A GLU* 3.9 35.4 + - - +
7A SER* 3.3 16.7 + - - +
38A SER* 3.1 8.8 + - - +
39A ASP* 1.3 80.1 - - + +
41A GLU* 1.3 57.1 + - - +
43A ILE* 4.4 6.5 - - + -
44A LEU* 2.8 31.9 + - - +
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Residues in contact with GLU 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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3A ILE* 4.5 5.4 - - + -
33A VAL* 3.8 19.5 - - - +
34A THR* 4.3 5.4 + - - +
36A PRO 4.8 0.3 - - - +
37A LEU* 3.4 22.1 - - + +
38A SER* 3.0 39.8 + - - +
40A GLN* 1.3 76.2 - - - +
42A ILE* 1.3 61.6 + - - +
44A LEU* 3.6 6.2 + - - +
45A GLY 3.3 10.4 + - - -
81A LYS* 2.7 44.4 + - + +
83A ILE* 4.4 6.9 - - + +
109A TYR* 2.8 23.9 + - + -
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Residues in contact with ILE 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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37A LEU* 3.9 28.7 - - + +
38A SER 3.2 14.7 + - - +
39A ASP* 3.1 14.7 + - - +
41A GLU* 1.3 75.4 - - - +
43A ILE* 1.3 67.5 + - + +
45A GLY 3.2 3.3 + - - -
46A GLU* 3.1 39.8 + - - +
109A TYR* 3.4 8.8 + - - +
154A LYS* 4.2 37.1 - - + +
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Residues in contact with ILE 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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7A SER* 3.5 31.9 - - - +
9A ALA* 6.2 0.2 - - - -
39A ASP* 2.9 31.9 + - + +
40A GLN* 3.8 8.1 - - + +
42A ILE* 1.3 78.8 - - + +
44A LEU* 1.3 51.3 + - - +
46A GLU* 3.0 18.5 + - + +
47A LYS* 2.7 52.9 + - + +
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Residues in contact with LEU 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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3A ILE* 4.0 16.2 - - + -
6A ILE* 4.0 22.2 - - + -
7A SER* 3.8 9.8 + - - +
13A ILE* 5.0 0.4 - - + -
40A GLN 2.8 19.1 + - - +
41A GLU 3.7 5.2 - - - +
42A ILE 3.2 0.2 - - - -
43A ILE* 1.3 76.9 - - - +
45A GLY* 1.3 57.1 + - - +
47A LYS* 3.1 4.8 + - - +
48A MET* 2.9 41.3 + - + +
74A ALA* 4.5 8.1 - - + -
77A LEU* 4.2 13.9 - - + -
79A ILE* 3.8 42.2 - - + -
83A ILE* 4.1 20.4 - - + -
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Residues in contact with GLY 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 GLU 3.3 4.6 + - - -
42A ILE 3.2 7.9 + - - -
44A LEU* 1.3 79.1 - - - +
46A GLU* 1.3 61.2 + - - +
48A MET* 3.3 13.4 + - - +
49A MET* 3.1 17.5 + - - +
83A ILE* 4.5 4.2 - - - +
107A ILE* 3.4 37.2 - - - +
109A TYR* 3.7 4.7 - - - -
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Residues in contact with GLU 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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42A ILE* 3.1 23.4 + - - +
43A ILE* 3.0 22.0 + - + +
45A GLY* 1.3 75.6 - - - +
47A LYS* 1.3 59.5 + - + +
49A MET* 3.4 2.9 + - - +
50A GLN* 2.9 29.0 + - - +
107A ILE* 4.1 11.4 - - + -
154A LYS* 3.0 31.3 + - - +
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Residues in contact with LYS 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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6A ILE* 3.5 19.5 - - + +
7A SER* 4.1 1.1 - - - -
8A LYS 2.9 25.0 + - - -
9A ALA* 3.0 18.1 + - - +
11A HIS 2.7 27.2 + - - +
12A LEU* 5.5 1.2 - - - +
13A ILE* 3.6 27.9 + - + +
43A ILE* 2.7 43.2 + - + +
44A LEU* 3.5 7.4 - - - +
46A GLU* 1.3 72.7 - - + +
48A MET* 1.3 58.0 + - - +
50A GLN* 3.2 10.0 + - + +
51A PHE* 2.9 24.6 + - - +
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Residues in contact with MET 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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13A ILE* 4.0 5.4 - - + -
44A LEU* 2.9 37.7 + - + +
45A GLY* 3.5 6.1 - - - +
47A LYS* 1.3 76.9 - - - +
49A MET* 1.3 61.2 + - - +
51A PHE* 3.2 7.1 + - - +
52A LEU* 3.2 23.9 + - - +
72A LEU* 3.3 38.2 - - + +
73A ALA 3.7 2.5 - - - -
74A ALA* 3.4 26.5 - - - +
77A LEU* 3.8 23.6 - - + -
83A ILE* 3.7 23.1 - - - +
84A ILE* 4.0 1.6 - - - -
85A ALA* 4.0 17.5 - - + +
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Residues in contact with MET 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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45A GLY 3.1 15.8 + - - +
46A GLU* 3.8 5.2 - - - +
48A MET* 1.3 71.9 - - - +
50A GLN* 1.3 66.8 + - - +
52A LEU* 3.1 6.9 + - - +
53A LYS* 3.0 38.7 + - - +
85A ALA* 4.1 4.7 - - + +
86A VAL 3.4 26.2 - - - +
87A LEU* 3.9 32.1 - - - -
105A GLU* 3.9 14.8 - - + +
106A ALA* 3.4 30.3 - - - +
107A ILE* 3.9 19.3 - - + -
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Residues in contact with GLN 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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12A LEU* 5.7 4.0 - - + -
46A GLU 2.9 15.0 + - - +
47A LYS* 3.3 15.5 - - + +
49A MET* 1.3 77.7 - - - +
51A PHE* 1.3 57.6 + - - +
53A LYS* 3.2 15.4 + - - +
54A HIS* 2.8 66.8 + - + -
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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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13A ILE* 3.6 40.6 - - + +
14A ASP* 4.4 3.6 - - - -
15A MET* 4.2 11.0 - - - -
18A ILE* 3.7 23.1 - - + -
47A LYS 2.9 12.7 + - - +
48A MET* 3.3 9.9 - - - +
50A GLN* 1.3 77.5 - - - +
52A LEU* 1.3 66.7 + - + +
54A HIS* 3.1 9.5 + - - +
55A SER* 2.7 43.7 + - - -
66A LEU* 3.7 27.6 - - + -
67A ARG 4.4 3.1 - - - -
69A GLY* 5.6 0.4 - - - -
72A LEU* 3.7 21.1 - - + -
131A LEU* 3.8 24.2 - - + -
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Residues in contact with LEU 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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48A MET 3.2 9.1 + - - +
49A MET* 3.1 11.0 + - - +
51A PHE* 1.3 94.8 - - + +
53A LYS* 1.3 62.7 + - - +
55A SER* 2.8 19.8 + - - -
56A GLN* 3.1 14.2 + - - +
69A GLY* 3.6 20.6 - - - +
71A GLY* 3.6 30.7 - - - +
72A LEU* 4.2 3.4 - - + -
85A ALA* 3.6 40.6 - - + +
86A VAL 4.1 0.4 - - - +
87A LEU* 3.8 30.7 - - + +
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Residues in contact with LYS 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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49A MET* 3.0 28.5 + - + +
50A GLN* 3.6 18.4 - - - +
52A LEU* 1.3 76.3 - - - +
54A HIS* 1.3 63.6 + - + +
56A GLN* 3.2 13.5 + - - +
57A ASP* 3.3 14.9 + - - +
87A LEU* 3.5 18.8 - - + -
102A TYR* 3.9 22.1 - - - +
105A GLU* 3.2 30.5 + - - -
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Residues in contact with HIS 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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12A LEU* 4.6 20.5 - - + +
13A ILE 5.3 2.6 + - - -
50A GLN* 2.8 58.5 + - + +
51A PHE* 3.5 10.4 - - - +
53A LYS* 1.3 79.3 - - + +
55A SER* 1.3 61.4 + - - +
57A ASP* 3.2 11.2 + - + +
60A MET* 3.6 21.2 - - + +
61A ALA 3.3 20.1 + - - -
64A MET* 3.2 35.2 - - + +
66A LEU* 3.8 7.8 - - + +
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Residues in contact with SER 55 (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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51A PHE* 2.7 28.7 + - - -
52A LEU* 2.8 18.2 + - - -
54A HIS* 1.3 73.1 - - - +
56A GLN* 1.3 57.5 + - - +
57A ASP 3.3 0.6 - - - -
61A ALA* 3.6 12.1 - - - +
66A LEU* 3.9 13.9 - - - +
67A ARG 3.3 22.7 - - - -
68A GLY* 3.4 15.4 - - - -
69A GLY* 3.0 23.0 + - - -
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Residues in contact with GLN 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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52A LEU 3.1 13.5 + - - +
53A LYS* 3.2 7.4 + - - +
54A HIS 3.1 0.4 - - - -
55A SER* 1.3 78.2 - - - +
57A ASP* 1.3 59.9 + - - +
58A PRO* 3.7 7.5 - - - +
68A GLY* 5.4 1.1 - - - -
69A GLY 2.8 30.8 + - - +
70A VAL* 3.9 5.1 - - + +
87A LEU* 3.0 35.4 + - + +
89A PRO* 3.2 25.9 - - + +
102A TYR* 3.8 18.5 - - - +
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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
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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