Contacts of the strand formed by residues 4 - 12 (chain A) in PDB entry 1XTR
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A PRO* 2.6 18.9 + - - +
3A GLN* 1.3 95.3 + - - +
5A LYS* 1.3 63.1 + - - +
6A SER* 5.1 0.2 + - - -
53A GLU* 3.6 10.6 + - - -
54A TYR 4.5 0.2 - - - -
55A HIS* 2.6 38.5 + - - -
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Residues in contact with LYS 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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2A PRO* 3.9 26.5 - - + -
4A SER* 1.3 77.3 + - - +
6A SER* 1.3 56.6 + - - +
7A ARG* 3.4 23.6 - - - +
52A GLN* 3.9 23.3 + - + +
53A GLU 3.2 6.0 + - - +
54A TYR* 3.3 37.7 + - + -
55A HIS* 2.5 35.9 + - - +
168A GLU* 5.6 1.6 - - - +
171A GLU* 3.5 20.0 + - - -
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Residues in contact with SER 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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4A SER* 5.1 0.3 + - - -
5A LYS* 1.3 73.0 - - - +
7A ARG* 1.3 80.0 + - - +
55A HIS* 3.2 25.9 - - - +
79A ASN* 4.0 2.9 + - - -
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Residues in contact with ARG 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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5A LYS* 3.4 37.4 + - - +
6A SER* 1.3 89.8 + - - +
8A LYS* 1.3 55.7 + - - +
9A ILE* 4.0 9.4 + - + -
54A TYR* 4.0 22.1 - - + -
55A HIS 2.9 6.5 + - - +
56A LEU* 3.3 21.2 - - + +
57A GLN* 2.7 33.1 + - - +
79A ASN* 3.0 28.6 - - + +
164A ILE* 5.3 4.9 - - + -
167A ALA* 5.4 9.5 - - + +
168A GLU 6.0 0.2 - - - +
171A GLU* 2.8 39.8 + - - -
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Residues in contact with LYS 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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7A ARG* 1.3 71.2 - - - +
9A ILE* 1.3 68.1 + - - +
57A GLN* 3.0 38.0 + - + +
59A VAL* 3.9 21.0 - - + +
76A ILE 5.1 0.4 - - - -
77A ASP* 3.2 36.3 - - - +
78A ILE* 3.5 23.1 - - + +
79A ASN* 2.6 39.7 + - - +
80A GLY 3.4 1.2 + - - -
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Residues in contact with ILE 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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7A ARG* 4.0 17.9 - - + +
8A LYS* 1.3 90.9 - - - +
10A ALA* 1.3 64.4 + - - +
11A ILE* 3.8 10.2 - - + +
56A LEU* 4.2 12.1 - - + -
57A GLN 2.8 9.3 + - - +
58A LEU* 3.3 17.6 - - + -
59A VAL* 2.7 33.4 + - - +
78A ILE* 4.5 0.9 - - - -
79A ASN* 4.6 0.9 - - + -
80A GLY* 3.4 22.2 - - - +
82A ILE* 3.7 29.8 - - + -
163A ILE* 4.2 21.5 - - + -
164A ILE* 5.1 2.9 - - + -
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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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9A ILE* 1.3 75.3 - - - +
11A ILE* 1.3 62.8 + - - +
12A LEU* 3.8 13.8 + - + +
59A VAL* 3.6 10.5 - - + +
61A THR* 4.7 4.0 - - + -
74A TYR* 5.1 5.6 - - + -
78A ILE* 3.9 26.8 - - + +
80A GLY 3.1 5.5 + - - -
81A TYR* 3.5 17.5 - - + +
82A ILE 2.9 24.9 + - - +
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Residues in contact with ILE 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 ILE* 3.8 20.4 - - + +
10A ALA* 1.3 75.8 - - - +
12A LEU* 1.3 55.1 + - - +
19A LYS* 3.7 39.0 - - + +
22A LEU* 6.1 3.1 - - + -
23A THR* 3.9 15.0 - - - +
58A LEU* 4.1 8.1 - - + -
59A VAL 3.0 22.6 + - - +
60A ASP* 4.4 5.4 - - - +
61A THR* 2.7 30.8 + - - -
82A ILE* 3.5 21.3 - - + +
84A VAL* 4.3 7.2 - - + -
160A PHE* 4.1 23.6 - - + -
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Residues in contact with LEU 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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10A ALA* 4.4 9.9 - - + +
11A ILE* 1.3 72.6 - - - +
13A GLY* 1.3 59.8 + - - +
19A LYS* 3.4 6.1 - - - -
61A THR* 3.4 34.1 - - + +
64A GLN* 4.4 12.1 - - - +
70A PHE* 4.0 23.1 - - + -
74A TYR* 4.1 15.7 - - + -
81A TYR* 3.5 31.2 - - + -
82A ILE 2.8 7.9 + - - +
83A LEU* 3.6 23.5 - - + -
84A VAL* 3.1 29.8 + - - +
96A ILE* 4.7 0.2 - - - -
99A ILE* 4.5 9.6 - - + -
103A LEU* 4.3 1.8 - - + -
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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