Contacts of the strand formed by residues 23 - 34 (chain A) in PDB entry 1XTE
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 23 (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* 3.1 10.3 - - - +
20A GLU* 2.8 67.6 + - + +
21A LYS* 3.4 9.9 - - - +
22A LYS* 1.3 75.2 - - - +
24A ARG* 1.3 67.9 + - - +
25A PHE* 4.1 20.9 - - + -
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Residues in contact with ARG 24 (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 GLU* 2.9 37.5 + - + -
18A HIS 3.5 4.7 - - - +
19A ARG* 3.7 27.6 - - + +
22A LYS 6.0 0.2 - - - -
23A LYS* 1.3 83.8 - - - +
25A PHE* 1.3 70.6 + - - +
74A ASP* 4.6 6.3 + - - -
76A PHE* 3.5 59.6 - - + +
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Residues in contact with PHE 25 (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 ASP 3.7 0.2 - - - +
17A GLU* 3.4 5.0 - - - +
18A HIS* 2.9 75.5 + - + +
20A GLU* 3.9 33.2 - - + -
23A LYS* 4.1 20.4 - - + -
24A ARG* 1.3 82.1 - - - +
26A THR* 1.3 62.6 - - - +
27A VAL* 3.8 16.4 - - + -
44A ARG* 4.1 24.2 - - - -
76A PHE* 3.8 8.3 - - - -
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Residues in contact with THR 26 (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 SER* 3.7 22.2 - - - +
16A ASP 3.5 7.0 - - - +
17A GLU* 5.1 2.6 - - - +
25A PHE* 1.3 75.8 - - - +
27A VAL* 1.3 62.6 + - - +
28A TYR* 3.7 35.8 - - + +
44A ARG* 3.4 24.1 - - - +
45A TYR 4.4 1.0 + - - -
75A ASN 4.9 1.0 + - - -
76A PHE* 3.3 25.6 - - - -
81A ILE* 3.9 18.2 - - + +
84A ARG* 6.4 0.2 - - - -
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Residues in contact with VAL 27 (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 SER* 3.2 2.8 - - - -
16A ASP* 2.9 37.9 + - + +
18A HIS* 3.7 36.8 - - + +
25A PHE* 3.8 17.0 - - + -
26A THR* 1.3 76.9 - - - +
28A TYR* 1.3 65.8 + - - +
29A LYS* 3.8 0.3 + - - +
42A PHE* 3.7 37.4 - - + -
43A ARG 3.9 9.2 - - - +
44A ARG* 4.2 8.3 - - + -
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Residues in contact with TYR 28 (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 ILE* 3.9 12.1 - - + -
14A SER 3.8 2.0 - - - -
15A SER* 3.8 19.5 - - - -
26A THR* 3.7 26.7 - - + +
27A VAL* 1.3 74.2 - - - +
29A LYS* 1.3 60.3 + - - +
30A VAL* 3.6 1.9 + - + +
41A VAL 3.6 0.9 - - - +
42A PHE* 3.4 5.9 - - - -
43A ARG 2.8 43.7 + - - +
45A TYR* 4.0 18.4 - - + -
48A PHE* 4.2 10.3 - + + -
81A ILE* 3.9 14.1 - - + +
84A ARG* 3.1 30.9 + - - +
85A ARG* 3.9 37.9 - - + -
88A LEU* 3.8 24.7 - - + -
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Residues in contact with LYS 29 (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 ILE* 3.4 8.4 - - - +
13A PRO* 3.2 29.2 - - + +
14A SER* 3.0 34.8 + - - +
16A ASP* 4.5 13.6 + - - +
27A VAL 3.8 1.4 + - - -
28A TYR* 1.3 71.1 - - - +
30A VAL* 1.3 60.2 + - - +
40A PHE* 3.6 44.6 - - + -
41A VAL 3.9 2.2 - - - -
42A PHE* 3.9 30.1 - - + -
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Residues in contact with VAL 30 (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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10A VAL* 4.7 1.3 - - + -
11A SER 3.5 6.5 - - - +
12A ILE* 4.1 9.4 - - + -
28A TYR 4.1 6.5 - - - +
29A LYS* 1.3 76.2 - - - +
31A LEU* 1.3 63.5 + - - +
32A VAL* 3.7 18.4 + - + +
40A PHE* 3.3 7.4 - - - -
41A VAL* 2.8 50.6 + - + +
43A ARG* 4.7 9.2 - - + -
48A PHE* 3.9 29.2 - - + -
92A ILE* 3.7 25.6 - - + -
110A PHE* 5.2 2.0 - - + -
111A LEU* 4.3 8.7 - - + -
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Residues in contact with LEU 31 (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 SER 3.8 0.5 - - - +
10A VAL* 3.2 6.8 - - - +
11A SER* 2.8 46.1 + - - +
13A PRO* 4.1 18.6 - - + -
29A LYS 3.9 1.8 + - - -
30A VAL* 1.3 70.8 - - - +
32A VAL* 1.3 60.9 + - - +
33A SER* 5.0 1.0 + - - -
38A GLU* 2.3 53.4 - - + +
39A TRP* 3.6 7.9 - - - +
40A PHE* 2.9 38.6 - - + -
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Residues in contact with VAL 32 (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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8A PRO* 5.2 2.5 - - + -
9A SER 3.7 2.7 - - - +
10A VAL* 4.3 10.8 - - + -
30A VAL* 3.9 18.4 - - + +
31A LEU* 1.3 76.3 - - - +
33A SER* 1.3 64.6 + - - +
34A VAL* 4.5 8.3 - - + -
38A GLU* 3.1 3.9 - - - -
39A TRP* 2.9 66.0 + - + +
41A VAL* 3.9 17.9 - - + -
111A LEU* 3.9 35.2 - - + +
113A MET* 4.8 2.2 - - + -
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Residues in contact with SER 33 (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 CYS 4.3 0.7 - - - +
8A PRO* 3.3 4.9 - - - +
9A SER* 2.8 53.8 + - - -
31A LEU* 5.0 1.6 + - - +
32A VAL* 1.3 74.0 + - - +
34A VAL* 1.3 64.8 + - - +
35A GLY 3.9 6.6 + - - -
37A SER 3.4 8.5 - - - -
38A GLU* 3.2 29.5 + - - -
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Residues in contact with VAL 34 (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 SER* 3.8 25.8 - - - +
8A PRO* 4.0 20.2 - - + -
32A VAL* 4.3 3.1 + - + -
33A SER* 1.3 78.8 - - - +
35A GLY* 1.3 66.1 + - - +
36A ARG 3.1 3.6 + - - -
37A SER* 2.9 22.2 + - - +
39A TRP* 3.6 30.6 - - + -
113A MET* 4.3 17.5 - - + -
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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