Contacts of the strand formed by residues 35 - 45 (chain A) in PDB entry 1XS2
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 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ARG* 3.4 68.8 + - + +
20A LEU 3.6 4.0 - - - -
21A PRO* 4.1 26.8 - - + +
22A LEU* 4.3 5.8 - - - +
34A THR* 1.3 111.5 + - - +
36A LYS* 1.3 62.9 + - - +
37A VAL* 6.0 0.4 - - - -
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Residues in contact with LYS 36 (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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18A ALA 3.5 0.2 - - - +
19A ARG* 3.4 3.2 - - - -
20A LEU* 2.8 37.6 + - - -
22A LEU* 4.2 6.3 - - + +
35A HIS* 1.3 75.0 - - - +
37A VAL* 1.3 79.6 + - - +
38A VAL* 3.6 9.5 + - + +
53A GLU* 3.9 15.6 + - - -
54A GLY 4.7 9.3 + - - -
55A THR* 5.4 6.5 - - - +
56A MET 6.2 0.2 - - - -
57A GLU* 6.3 3.6 - - - -
298A MET* 4.1 13.3 + - - -
299A LEU* 3.5 43.4 + - + +
330A TRP* 3.8 24.5 - - + -
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Residues in contact with VAL 37 (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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17A VAL* 3.6 26.7 - - + -
18A ALA 3.2 4.3 - - - +
19A ARG* 4.3 17.3 - - + +
35A HIS 6.0 0.4 - - - -
36A LYS* 1.3 88.1 + - - +
38A VAL* 1.3 61.0 + - - +
39A PRO* 3.4 10.2 - - + +
56A MET 5.3 1.6 - - - +
58A ALA* 6.1 3.8 - - + -
67A ILE* 3.5 31.8 - - + +
368A GLU* 5.1 3.6 - - - +
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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
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16A VAL 3.6 1.9 - - - +
17A VAL* 3.6 2.2 - - - -
18A ALA* 2.7 36.9 + - + +
20A LEU* 4.2 25.1 - - + -
36A LYS* 3.8 22.9 - - - +
37A VAL* 1.3 75.5 - - - +
39A PRO* 1.3 60.5 - - - +
40A LEU* 3.7 9.8 + - + +
53A GLU* 3.6 37.0 - - + +
301A SER* 3.9 11.2 - - - +
330A TRP* 4.7 7.0 - - + -
334A LEU* 4.2 13.7 - - + -
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Residues in contact with PRO 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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15A ILE* 5.6 0.7 - - + -
16A VAL 3.6 5.2 - - - +
17A VAL* 4.2 14.8 - - + -
36A LYS* 5.4 0.4 - - - +
37A VAL* 3.4 12.8 - - + +
38A VAL* 1.3 83.4 - - + +
40A LEU* 1.3 60.2 + - - +
53A GLU* 3.5 4.5 - - - +
54A GLY* 2.8 57.4 + - - +
56A MET* 4.2 15.5 - - - +
67A ILE* 4.4 13.2 - - + -
71A LEU* 4.5 23.6 - - + -
109A MET* 3.9 4.9 - - + +
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Residues in contact with LEU 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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14A GLU 3.6 0.2 - - - +
15A ILE* 3.4 10.6 - - - +
16A VAL* 2.7 43.8 + - + +
38A VAL* 4.3 15.0 - - + +
39A PRO* 1.3 76.1 - - - +
41A LEU* 1.3 60.0 + - - +
42A ILE* 5.0 3.8 - - + -
51A VAL* 4.3 6.7 - - + -
52A ALA 3.3 15.0 - - - +
53A GLU* 3.9 19.1 - - + +
109A MET* 4.0 3.4 - - - -
301A SER* 4.7 0.9 - - - +
303A ILE* 3.9 19.3 - - + -
334A LEU* 4.4 7.4 - - + -
358A LEU* 4.0 30.1 - - + -
363A LEU* 4.2 25.4 - - + -
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Residues in contact with LEU 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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13A ALA* 4.1 11.7 - - + -
14A GLU 3.4 16.4 - - - +
15A ILE* 4.2 12.1 - - + -
40A LEU* 1.3 73.8 - - - +
42A ILE* 1.3 65.4 + - - +
43A LEU* 4.1 17.9 - - + -
50A GLY 3.6 0.7 - - - +
51A VAL* 3.2 7.1 - - - +
52A ALA 2.9 33.4 + - - +
74A LEU* 4.4 7.4 - - + -
79A LEU* 4.1 19.1 - - + -
109A MET* 3.5 49.7 - - + +
110A VAL* 3.8 20.2 - - + +
113A ALA* 4.1 1.7 - - + +
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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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12A ALA 3.8 0.3 - - - +
13A ALA* 3.1 5.7 - - - -
14A GLU* 2.8 54.7 + - + +
16A VAL* 4.6 11.7 - - + -
40A LEU* 5.0 5.4 - - + -
41A LEU* 1.3 81.0 - - - +
43A LEU* 1.3 61.7 - - - +
44A HIS* 3.6 22.1 - - + +
49A GLN* 3.9 24.2 - - + +
50A GLY 3.3 7.9 - - - +
51A VAL* 4.0 10.8 - - + -
358A LEU* 3.7 26.5 - - + -
360A ARG* 3.9 22.2 - - - +
363A LEU* 5.3 0.7 - - + -
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Residues in contact with LEU 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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10A ILE* 4.2 22.4 - - + -
12A ALA 3.6 0.4 - - - -
13A ALA* 3.7 26.0 - - + -
41A LEU* 4.2 10.8 - - + -
42A ILE* 1.3 73.9 - - - +
44A HIS* 1.3 61.7 + - - +
49A GLN* 3.1 5.2 - - - +
50A GLY 2.7 41.2 + - - +
79A LEU* 4.3 9.2 - - + -
82A ILE* 4.5 7.6 - - + -
110A VAL* 3.7 35.4 - - + +
113A ALA* 3.7 17.3 - - + +
114A ALA* 3.8 12.8 - - + +
117A LEU* 4.0 15.1 - - + +
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Residues in contact with HIS 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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10A ILE* 3.6 5.7 - - - +
11A GLU* 3.0 27.3 + - + +
12A ALA* 2.8 40.5 + - + +
14A GLU* 2.8 33.2 + - + -
42A ILE* 3.6 16.0 - - + +
43A LEU* 1.3 73.6 - - - +
45A GLY* 1.3 58.9 + - - +
48A VAL 3.7 5.2 + - - +
49A GLN* 3.2 37.1 + - + +
117A LEU* 4.6 3.4 - - - -
360A ARG* 5.3 1.6 - - - -
372A GLU* 6.0 0.7 - - - -
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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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9A LYS 3.3 15.5 - - - -
11A GLU* 4.1 10.1 + - - -
44A HIS* 1.3 75.6 - - - +
46A GLU* 1.3 65.9 + - - +
47A GLY 3.1 3.6 - - - -
48A VAL* 2.9 37.9 + - - +
117A LEU* 4.0 8.8 - - - +
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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