Contacts of the helix formed by residues 36 - 50 (chain A) in PDB entry 1XD7
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 ASN 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A THR* 1.3 76.3 - - + +
37A PRO* 1.3 94.8 - - - +
38A VAL* 2.7 41.5 + - - +
39A VAL* 3.3 17.8 - - + +
40A VAL* 3.2 26.2 + - - +
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Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 4.9 0.7 - - - +
27A GLU* 4.6 15.0 - - + +
30A ALA* 3.6 20.6 - - + -
35A THR 3.7 5.6 - - - +
36A ASN* 1.3 90.2 - - - +
38A VAL* 1.3 54.5 + - + +
39A VAL 3.4 0.2 - - - -
40A VAL* 3.9 6.0 - - + +
41A ARG* 2.6 45.3 + - + +
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASN* 2.7 41.8 - - - +
37A PRO* 1.3 73.8 - - + +
39A VAL* 1.3 70.9 + - + +
41A ARG* 3.2 9.5 + - - +
42A ARG* 2.8 36.7 + - - +
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Residues in contact with VAL 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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10A VAL* 4.4 10.3 - - + -
35A THR* 4.0 16.2 - - + -
36A ASN* 3.3 28.9 - - + +
38A VAL* 1.3 88.1 - - + +
40A VAL* 1.3 53.9 + - - +
42A ARG* 3.1 8.6 + - - +
43A MET* 2.7 57.8 + - + +
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Residues in contact with VAL 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL* 5.5 0.9 - - + -
14A ILE* 4.1 19.3 - - + -
26A SER* 3.8 19.7 - - - +
29A ILE* 4.0 15.9 - - + -
30A ALA* 3.5 24.2 - - + -
33A VAL* 5.4 1.8 - - + -
35A THR* 4.4 11.2 - - + -
36A ASN 3.2 17.4 + - - +
37A PRO* 4.0 7.4 - - + +
38A VAL 3.2 0.6 - - - -
39A VAL* 1.3 77.7 - - + +
41A ARG* 1.3 57.5 + - - +
43A MET* 3.3 1.2 + - - +
44A ILE* 2.8 53.1 + - + +
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Residues in contact with ARG 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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26A SER* 3.4 26.8 + - - +
27A GLU* 4.4 13.1 - - - +
37A PRO* 2.6 30.6 + - - +
38A VAL* 3.2 8.8 + - - +
40A VAL* 1.3 75.9 - - - +
42A ARG* 1.3 53.6 + - - +
44A ILE* 3.0 10.9 + - - +
45A SER* 2.6 36.7 + - - -
190A SO4 2.6 36.1 + - - -
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Residues in contact with ARG 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 5.6 7.4 - - - +
38A VAL 2.8 17.6 + - - +
39A VAL* 3.2 11.2 - - - +
41A ARG* 1.3 69.3 - - - +
43A MET* 1.3 70.4 + - + +
45A SER* 2.9 25.3 + - - -
46A LEU* 3.0 52.1 + - + +
49A LYS* 6.2 0.4 - - - +
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Residues in contact with MET 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 ARG* 3.1 54.3 - - + +
10A VAL* 4.1 12.1 - - + -
11A ALA* 5.0 2.0 - - - +
14A ILE* 3.7 22.4 - - + -
39A VAL* 2.7 39.2 + - + +
40A VAL 3.6 4.3 - - - +
42A ARG* 1.3 75.0 - - + +
44A ILE* 1.3 57.2 + - - +
46A LEU* 3.3 14.0 + - - +
47A LEU* 2.9 38.9 + - + +
80A VAL* 3.9 20.4 - - + +
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Residues in contact with ILE 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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14A ILE* 4.0 24.9 - - + -
18A ILE* 4.8 4.5 - - + -
26A SER* 4.2 18.2 - - - +
29A ILE* 4.5 11.9 - - + -
40A VAL* 2.8 40.0 + - + +
41A ARG* 3.0 6.9 + - - +
43A MET* 1.3 74.8 - - - +
45A SER* 1.3 64.1 + - - +
47A LEU* 4.0 5.9 - - - +
48A LYS* 3.1 39.8 + - + +
53A LEU* 4.2 15.0 - - + -
61A GLY* 6.0 4.7 - - - -
62A ALA* 5.0 7.9 - - + +
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Residues in contact with SER 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 ARG 2.6 19.4 + - - -
42A ARG* 3.1 20.0 + - - -
44A ILE* 1.3 70.9 - - - +
46A LEU* 1.3 58.6 + - - +
48A LYS* 3.3 12.4 + - - +
49A LYS* 2.7 38.1 + - - +
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Residues in contact with LEU 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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7A ARG* 5.2 9.6 - - - +
42A ARG* 3.0 59.5 + - + +
43A MET* 3.5 15.7 - - - +
45A SER* 1.3 77.6 - - - +
47A LEU* 1.3 52.7 + - - +
49A LYS* 2.9 20.9 + - + +
50A ALA* 2.7 36.5 + - - +
79A ALA* 3.6 25.8 - - - +
80A VAL* 4.5 14.8 - - + -
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Residues in contact with LEU 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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11A ALA* 4.5 15.3 - - + +
14A ILE* 4.6 8.5 - - + -
15A LEU* 4.1 34.1 - - + -
43A MET* 2.9 29.2 + - + +
44A ILE* 4.0 2.2 - - - +
46A LEU* 1.3 74.9 - - - +
48A LYS* 1.3 54.9 + - - +
50A ALA* 3.4 5.0 + - - +
51A ASP 3.3 2.6 + - - -
52A ILE* 2.7 60.3 + - + +
53A LEU* 3.7 24.9 - - + -
76A VAL* 4.3 12.1 - - + -
79A ALA* 4.4 7.4 - - + -
80A VAL* 4.5 8.1 - - + -
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Residues in contact with LYS 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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44A ILE* 3.1 33.7 + - + +
45A SER* 3.7 11.9 - - - +
46A LEU 3.1 0.4 - - - -
47A LEU* 1.3 71.9 - - - +
49A LYS* 1.3 57.8 + - - +
50A ALA 3.0 1.8 - - - -
51A ASP* 2.4 34.7 + - - +
53A LEU* 3.1 35.5 - - + +
55A SER* 3.7 36.9 + - - +
62A ALA* 4.4 5.6 - - + +
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Residues in contact with LYS 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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42A ARG* 6.2 0.2 - - - +
45A SER* 2.7 23.5 + - - +
46A LEU* 3.1 24.7 - - + +
48A LYS* 1.3 71.8 - - - +
50A ALA* 1.3 55.3 + - - +
51A ASP* 3.1 8.5 + - - +
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Residues in contact with ALA 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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46A LEU 2.7 9.7 + - - +
47A LEU 3.7 4.3 - - - +
48A LYS 3.0 0.4 - - - -
49A LYS* 1.3 74.7 - - - +
51A ASP* 1.3 69.0 + - - +
52A ILE* 2.9 13.2 + - + +
75A GLU* 5.5 0.9 - - - +
79A ALA* 3.3 36.3 - - + -
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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