Contacts of the strand formed by residues 9 - 20 (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 SER 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A CYS 3.6 2.9 + - - -
8A PRO* 1.3 75.0 - - - +
10A VAL* 1.3 65.6 + - - +
31A LEU 3.8 0.5 - - - +
32A VAL* 4.5 0.2 - - - +
33A SER* 2.8 53.7 + - - -
96A VAL* 4.7 2.5 - - - -
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Residues in contact with VAL 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 PRO* 5.1 0.7 - - + -
9A SER* 1.3 83.1 - - - +
11A SER* 1.3 62.3 + - - +
30A VAL* 4.7 1.6 - - + -
31A LEU 3.2 9.9 - - - +
32A VAL* 4.3 12.3 - - + -
92A ILE* 3.6 38.1 - - + +
93A GLN* 2.8 44.1 + - + +
96A VAL* 4.0 22.3 - - + +
111A LEU* 4.2 20.6 - - + -
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Residues in contact with SER 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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10A VAL* 1.3 76.9 - - - +
12A ILE* 1.3 63.8 + - - +
13A PRO* 3.5 8.9 - - - +
30A VAL* 3.5 4.9 - - - +
31A LEU* 2.8 49.6 + - - +
89A ASN* 3.2 11.4 - - - +
93A GLN* 4.2 4.9 - - - -
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Residues in contact with ILE 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 SER* 1.3 79.7 - - - +
13A PRO* 1.3 61.9 - - - +
14A SER 4.0 1.6 - - - +
28A TYR* 3.9 19.7 - - + -
29A LYS 3.4 13.7 - - - +
30A VAL* 4.1 4.3 - - + -
48A PHE* 3.7 20.6 - - + -
85A ARG* 2.9 44.5 + - + +
88A LEU* 3.7 11.2 - - + -
89A ASN* 3.1 43.3 + - + +
92A ILE* 3.7 22.7 - - + -
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Residues in contact with PRO 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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11A SER* 3.5 16.2 - - - +
12A ILE* 1.3 89.1 - - - +
14A SER* 1.3 66.9 + - - +
29A LYS* 3.2 23.1 - - + +
31A LEU* 4.1 24.5 - - + +
40A PHE* 5.1 0.2 - - + -
85A ARG* 3.3 17.6 + - - +
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Residues in contact with SER 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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12A ILE* 3.3 2.3 + - - +
13A PRO* 1.3 84.9 - - - +
15A SER* 1.3 65.8 + - - +
16A ASP* 4.7 3.0 + - - -
28A TYR* 3.8 1.0 - - - -
29A LYS* 3.0 54.6 + - - +
85A ARG* 3.6 17.2 - - - +
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Residues in contact with SER 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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14A SER* 1.3 79.7 - - - +
16A ASP* 1.3 72.9 + - - +
26A THR* 3.7 18.1 - - - +
27A VAL 3.2 13.0 - - - -
28A TYR* 3.8 15.7 - - - -
29A LYS 4.5 0.4 - - - +
81A ILE* 3.6 20.7 - - - +
85A ARG* 4.2 5.5 + - - +
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Residues in contact with ASP 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 SER* 4.7 2.5 + - - -
15A SER* 1.3 83.6 - - - +
17A GLU* 1.3 61.7 + - - +
18A HIS* 3.8 19.6 + - + +
25A PHE 3.7 0.3 - - - +
26A THR* 3.5 5.8 - - - -
27A VAL* 2.9 37.4 + - + +
29A LYS* 4.5 19.8 - - - +
42A PHE* 5.3 5.2 - - - -
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Residues in contact with GLU 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 ASP* 1.3 75.5 - - - +
18A HIS* 1.3 74.6 + - - +
19A ARG* 5.1 8.3 + - - +
24A ARG* 2.9 45.1 + - + -
25A PHE 3.4 9.6 - - - +
26A THR* 4.6 4.0 - - + +
76A PHE* 4.1 14.2 - - + +
81A ILE* 6.5 0.9 - - + -
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Residues in contact with HIS 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 ASP* 3.8 20.3 + - + +
17A GLU* 1.3 87.7 - - - +
19A ARG* 1.3 63.6 + - - +
24A ARG* 3.5 2.8 - - - -
25A PHE* 2.9 65.1 + + + +
27A VAL* 3.7 21.5 - - + +
42A PHE* 6.4 0.7 - + - -
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Residues in contact with ARG 19 (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* 5.1 7.0 + - - +
18A HIS* 1.3 78.8 - - - +
20A GLU* 1.3 83.3 + - - +
22A LYS* 5.7 1.6 - - - +
23A LYS 3.1 12.6 - - - +
24A ARG* 3.7 27.1 - - + +
25A PHE* 4.9 0.7 - - - -
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Residues in contact with GLU 20 (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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19A ARG* 1.3 88.6 - - - +
21A LYS* 1.3 69.1 + - - +
22A LYS 2.9 1.7 + - - -
23A LYS* 2.8 51.5 + - + +
25A PHE* 3.9 22.5 - - + -
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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