Contacts of the strand formed by residues 9 - 18 (chain A) in PDB entry 1XSA
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 ARG 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A LEU* 1.3 87.3 - - + +
10A ALA* 1.3 65.9 + - - +
11A CYS* 4.8 0.2 - - - -
49A HIS* 3.5 3.4 + - - -
50A VAL* 3.2 32.2 + - + +
56A ASP* 2.8 44.3 + - - +
84A GLU* 6.2 0.2 - - - -
95A THR* 3.3 21.5 - - + -
97A ILE* 4.4 8.3 - - + +
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Residues in contact with ALA 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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8A LEU 4.2 0.4 - - - -
9A ARG* 1.3 67.3 - - - +
11A CYS* 1.3 67.6 + - - +
47A LYS* 5.4 2.2 - - + -
48A GLY* 3.2 20.9 - - - +
49A HIS* 3.5 12.3 - - - +
94A LYS* 3.7 25.9 - - + +
95A THR 2.3 27.2 + - - +
96A VAL* 3.1 7.9 - - + -
97A ILE* 2.8 27.9 + - - +
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Residues in contact with CYS 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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9A ARG* 4.3 1.3 - - - -
10A ALA* 1.3 84.5 - - - +
12A GLY* 1.3 58.7 + - - +
47A LYS* 4.0 4.0 - - - -
48A GLY 3.1 22.0 + - - +
50A VAL* 3.7 10.1 - - - -
56A ASP* 2.7 49.8 - - - +
59A THR* 2.9 21.6 - - + +
60A ALA* 3.2 14.6 - - - +
96A VAL* 4.9 0.4 - - - -
97A ILE* 3.5 9.6 - - + +
99A TRP* 3.7 11.4 - - + -
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Residues in contact with GLY 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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11A CYS* 1.3 75.4 - - - +
13A LEU* 1.3 58.7 + - - -
45A PRO* 6.2 0.2 - - - -
46A PRO 3.6 5.4 - - - -
47A LYS* 3.4 20.3 - - - +
60A ALA* 3.2 18.6 - - - +
97A ILE 2.6 22.6 + - - +
98A TYR* 4.1 6.5 - - - -
99A TRP* 3.2 14.0 + - - -
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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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12A GLY* 1.3 77.0 - - - +
14A ILE* 1.3 55.9 + - - +
15A ILE* 2.6 32.6 + - + +
45A PRO* 4.0 14.2 - - - +
46A PRO* 3.7 9.5 + - - +
57A LEU* 3.7 11.9 - - + -
60A ALA* 3.9 4.7 - - + +
61A LEU* 3.4 22.7 - - + -
64A THR* 2.7 41.7 - - + +
75A LEU* 4.1 9.6 - - + -
77A ILE* 3.6 18.6 - - + -
98A TYR* 4.8 1.3 - - - -
99A TRP* 3.5 28.3 - - + +
101A ALA* 4.4 6.7 - - + -
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Residues in contact with ILE 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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13A LEU* 1.3 64.5 - - - +
15A ILE* 1.3 59.5 + - - +
16A PHE* 3.5 2.3 + - + -
31A PHE* 3.9 27.6 - - + -
45A PRO* 4.5 6.5 - - + -
98A TYR* 3.3 48.9 - - + +
99A TRP 2.3 32.1 + - - +
100A LEU* 3.5 24.9 - - + -
101A ALA 3.0 21.1 + - - +
136A MET* 4.4 11.4 - - + -
139A ALA* 4.4 17.3 - - + +
140A LEU* 4.5 8.7 - - + -
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Residues in contact with ILE 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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13A LEU* 2.6 27.8 + - + +
14A ILE* 1.3 72.7 - - - +
16A PHE* 1.3 64.9 + - - +
31A PHE* 3.5 6.2 - - - +
32A LEU* 3.0 37.4 + - + +
45A PRO* 5.1 3.2 - - - +
46A PRO* 3.6 16.8 - - + -
64A THR* 3.2 29.6 - - + -
70A ILE* 3.3 20.4 - - + -
75A LEU* 4.3 5.4 - - + -
101A ALA* 3.9 9.2 - - + +
103A VAL* 4.1 11.9 - - + -
121A TRP* 3.3 27.8 - - + -
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Residues in contact with PHE 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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14A ILE 3.7 9.6 - - - -
15A ILE* 1.3 78.4 - - - +
17A ARG* 1.3 62.0 + - - +
18A ARG* 4.6 4.5 - - - -
29A ILE* 3.7 24.5 - - + -
30A GLU 2.8 18.2 - - - +
31A PHE* 3.5 17.3 - + + -
78A ILE* 3.7 8.7 - - + -
100A LEU* 4.3 9.0 - - + -
101A ALA 2.8 42.9 + - - +
102A GLU* 3.3 39.8 - - + -
103A VAL 3.6 3.3 + - - -
121A TRP* 3.4 7.2 - - - -
147A LEU* 3.2 44.0 - - + -
150A ILE* 5.6 1.3 - - + -
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Residues in contact with ARG 17 (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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16A PHE* 1.3 78.0 - - - +
18A ARG* 1.3 69.5 + - - +
19A CYS* 4.6 0.6 - - - -
28A ALA 3.0 4.3 - - - +
30A GLU* 2.8 58.2 + - - +
102A GLU* 4.7 1.3 - - - -
103A VAL* 3.5 27.6 - - + +
106A TYR* 2.5 83.3 + - + +
108A VAL* 5.8 0.4 - - - -
121A TRP* 3.2 51.7 - - + +
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Residues in contact with ARG 18 (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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16A PHE* 4.3 8.0 - - + -
17A ARG* 1.3 80.9 - - - +
19A CYS* 1.3 72.3 + - - +
28A ALA* 2.9 7.6 - - + -
29A ILE* 3.7 25.8 - - + +
102A GLU* 2.4 43.3 + - - +
106A TYR* 4.8 3.8 - - - -
150A ILE* 5.2 4.0 - - - -
151A GLU* 2.3 62.7 + - - +
152A ALA* 5.1 1.9 - - - +
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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