Contacts of the helix formed by residues 2 - 16 (chain A) in PDB entry 1XBN
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 LYS 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 72.7 - - - +
3A GLY* 1.3 70.9 + - - +
4A THR* 3.4 14.5 + - - +
5A ILE* 3.5 10.6 - - + +
6A VAL* 3.1 22.7 + - - +
40A LEU* 3.9 22.8 + - + +
41A GLU 3.9 3.1 - - - +
42A ASP* 3.5 24.0 + - - +
43A ILE* 3.2 5.4 - - - -
105A LEU* 6.0 4.0 - - + -
109A ILE* 3.4 27.1 - - + +
110A LYS 3.0 27.5 + - - -
111A GLY* 4.7 1.6 - - - -
112A ALA* 4.0 14.5 - - - +
200A HEM 3.8 22.8 + - + +
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Residues in contact with GLY 3 (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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2A LYS* 1.3 75.7 - - - +
4A THR* 1.3 65.7 + - - +
6A VAL* 3.2 5.9 + - - +
7A GLY* 3.1 12.1 + - - -
36A VAL* 4.0 7.7 - - - +
37A ILE* 3.4 18.1 - - - +
38A THR 4.5 0.2 - - - -
41A GLU 2.7 28.3 + - - -
43A ILE* 3.1 13.7 - - - +
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Residues in contact with THR 4 (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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2A LYS* 3.4 8.4 - - - +
3A GLY* 1.3 74.1 - - - +
5A ILE* 1.3 57.1 + - - +
7A GLY* 2.3 34.9 + - - -
8A THR* 3.3 5.0 + - + +
38A THR* 3.6 18.9 + - + +
39A PRO 3.4 22.4 + - - +
40A LEU* 4.5 4.3 - - - -
81A TRP* 4.5 11.8 - - + -
200A HEM 6.2 2.9 - - - -
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Residues in contact with ILE 5 (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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1A MET* 3.1 29.4 - - + -
2A LYS* 3.5 15.4 - - + +
4A THR* 1.3 78.9 - - - +
6A VAL* 1.3 61.6 + - - +
8A THR* 2.5 34.6 + - - -
9A TRP* 3.3 31.3 + - + -
78A PHE* 3.3 38.8 - - + -
198A OXY 3.7 4.9 - - - +
200A HEM 3.6 47.1 - - + +
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Residues in contact with VAL 6 (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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1A MET* 3.9 25.4 - - + -
2A LYS 3.1 16.8 - - - +
3A GLY 3.2 8.9 + - - +
4A THR 2.9 0.6 + - - -
5A ILE* 1.3 72.6 - - - +
7A GLY* 1.3 68.2 + - - +
9A TRP* 3.5 16.2 + - + +
10A ILE* 3.4 25.8 + - + +
36A VAL* 3.8 15.9 - - + -
43A ILE* 3.3 35.2 - - + -
48A VAL* 4.7 11.9 - - + -
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Residues in contact with GLY 7 (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 GLY 3.1 6.7 + - - -
4A THR* 2.3 26.0 + - - -
6A VAL* 1.3 70.9 - - - +
8A THR* 1.3 56.0 + - - -
10A ILE* 3.3 7.5 + - - +
11A LYS* 2.9 27.2 + - - +
36A VAL* 5.1 5.6 - - - +
37A ILE 5.6 0.2 - - - -
38A THR* 5.2 9.4 - - - -
81A TRP* 3.7 13.4 - - - -
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Residues in contact with THR 8 (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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4A THR* 4.2 5.8 - - + +
5A ILE* 2.5 25.0 + - - +
7A GLY* 1.3 73.9 - - - +
9A TRP* 1.3 81.2 + - - +
11A LYS* 3.0 2.9 + - - -
12A THR* 2.5 36.4 + - - -
74A ASN* 3.1 21.7 + - - +
77A THR* 3.7 7.6 - - + -
78A PHE* 4.1 17.9 - - + -
81A TRP* 3.2 33.8 - - + -
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Residues in contact with TRP 9 (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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1A MET* 3.5 23.7 - - + +
5A ILE* 3.3 30.0 + - + -
6A VAL* 3.7 19.7 - - + +
7A GLY 3.3 0.2 - - - -
8A THR* 1.3 108.0 + - - +
10A ILE* 1.3 52.8 + - + +
12A THR* 4.2 1.6 - - - -
13A LEU* 2.6 43.2 + - + +
48A VAL* 4.2 17.0 - - + +
52A PHE* 4.5 12.6 - - + -
67A TRP* 3.7 31.0 - + - -
70A VAL* 4.0 11.1 - - + +
74A ASN* 3.5 14.4 - - - +
137A MET* 5.5 3.7 - - + +
140A TYR* 2.3 59.7 - + - -
200A HEM 5.2 4.7 - + + -
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Residues in contact with ILE 10 (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 VAL* 3.4 21.3 + - + +
7A GLY* 3.3 6.6 + - - +
8A THR 3.2 0.4 - - - -
9A TRP* 1.3 77.9 - - + +
11A LYS* 1.3 62.6 + - - +
13A LEU* 3.0 7.0 + - + +
14A ARG* 2.8 35.5 + - + +
23A ASP* 4.4 2.9 - - - +
27A LYS* 3.6 50.0 - - + +
36A VAL* 3.6 28.0 - - + +
51A ILE* 5.4 11.7 - - + -
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Residues in contact with LYS 11 (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 GLY 2.9 14.7 + - - +
8A THR* 3.0 7.2 + - - +
10A ILE* 1.3 76.3 - - - +
12A THR* 1.3 54.0 + - - +
14A ARG* 3.2 2.7 + - - +
15A ASP* 2.5 60.8 + - + +
77A THR* 3.5 27.9 + - + +
80A GLU* 2.7 30.7 + - - -
81A TRP* 3.7 38.8 - - + +
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Residues in contact with THR 12 (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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8A THR 2.5 12.5 + - - -
9A TRP 4.2 1.1 - - - -
11A LYS* 1.3 72.6 - - - +
13A LEU* 1.3 59.7 + - - +
14A ARG 3.2 0.7 + - - -
15A ASP* 3.2 14.6 + - - -
16A LEU 3.6 1.2 + - - -
17A TYR* 2.9 41.2 - - + -
70A VAL* 3.5 36.1 - - + +
73A GLN* 3.9 2.9 - - + -
74A ASN* 2.5 30.0 + - - +
77A THR* 2.2 31.9 + - - -
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Residues in contact with LEU 13 (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 TRP 2.6 28.5 + - - +
10A ILE* 3.0 10.1 + - + +
12A THR* 1.3 74.9 - - - +
14A ARG* 1.3 58.6 + - + +
17A TYR* 2.5 47.9 - - + +
23A ASP* 3.2 33.1 - - + +
51A ILE* 3.9 19.1 - - + -
52A PHE* 3.9 26.9 - - + -
55A VAL* 4.2 22.4 - - + -
66A ILE* 5.0 7.0 - - + -
70A VAL* 4.9 6.3 - - + -
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Residues in contact with ARG 14 (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 ILE* 2.8 21.6 + - + +
11A LYS* 4.1 2.2 - - - +
13A LEU* 1.3 77.0 - - - +
15A ASP* 1.3 69.6 + - - +
16A LEU* 2.9 4.8 + - - -
17A TYR 3.5 6.0 + - - +
18A GLY 3.9 8.7 - - - +
19A ASN* 3.6 21.7 - - - -
20A ASP* 3.4 27.4 + - - +
23A ASP* 3.0 28.7 + - - +
24A GLU* 2.6 60.1 + - - +
27A LYS* 3.6 30.3 - - - +
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Residues in contact with ASP 15 (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 LYS* 2.5 54.7 + - + +
12A THR* 3.2 9.8 + - - +
14A ARG* 1.3 72.3 - - - +
16A LEU* 1.3 81.3 + - - +
73A GLN* 3.9 20.4 + - + +
77A THR* 5.2 0.7 - - - -
80A GLU* 4.7 5.9 - - - +
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Residues in contact with LEU 16 (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 THR 3.6 2.6 + - - -
14A ARG 3.7 1.8 - - - -
15A ASP* 1.3 94.5 - - - +
17A TYR* 1.3 77.9 + - + +
18A GLY 3.8 5.5 + - - -
73A GLN* 3.3 23.6 - - - +
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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