Contacts of the strand formed by residues 52 - 61 (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 GLN 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PRO* 2.9 34.2 + - - +
3A GLN* 3.4 6.7 + - - +
5A LYS* 3.9 26.4 + - + +
48A THR* 3.3 1.4 - - - -
49A VAL 2.7 38.4 + - - +
50A ASN* 3.1 4.4 + - + +
51A GLY* 1.3 76.7 - - - +
53A GLU* 1.3 86.8 + - - +
54A TYR* 3.3 30.6 - - + +
168A GLU* 5.1 1.3 - - - +
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Residues in contact with GLU 53 (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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3A GLN* 3.4 35.5 + - - +
4A SER* 3.6 7.7 - - - -
5A LYS 3.2 11.1 + - - -
46A LEU* 3.1 45.2 - - + +
47A ILE 4.4 2.7 - - - +
48A THR* 3.7 16.4 - - - +
51A GLY 3.6 4.0 + - - +
52A GLN* 1.3 97.7 + - - +
54A TYR* 1.3 66.1 + - - +
55A HIS* 4.4 1.4 + - - -
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Residues in contact with TYR 54 (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* 3.3 43.4 + - + +
7A ARG* 4.0 25.8 - - + -
46A LEU* 3.4 11.4 - - - +
47A ILE 2.8 38.8 + - - +
49A VAL* 3.8 14.8 - - + -
52A GLN* 3.3 43.0 - - + +
53A GLU* 1.3 73.2 - - - +
55A HIS* 1.3 64.0 + - - +
56A LEU* 3.7 17.7 - - + -
164A ILE* 3.4 31.0 - - + -
168A GLU* 2.7 33.1 + - + +
171A GLU* 5.7 0.2 - - - -
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Residues in contact with HIS 55 (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* 2.6 33.1 + - - -
5A LYS 2.5 14.1 + - - +
6A SER* 3.2 18.6 - - - +
7A ARG 2.9 24.9 + - - +
44A THR* 4.5 19.0 - - + +
45A LYS 4.0 3.4 - - - -
46A LEU* 3.1 32.0 - - + +
53A GLU* 4.4 1.6 + - - -
54A TYR* 1.3 69.8 - - - +
56A LEU* 1.3 60.8 + - - +
57A GLN* 3.7 2.1 + - - +
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Residues in contact with LEU 56 (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* 3.3 25.4 - - + +
9A ILE* 4.2 10.1 - - + -
26A PHE* 4.2 15.9 - - + -
43A PHE 3.6 1.0 - - - +
44A THR* 3.2 7.0 - - - +
45A LYS* 2.8 44.2 + - + +
47A ILE* 3.5 27.4 - - + -
54A TYR* 4.3 8.1 - - + -
55A HIS* 1.3 70.5 - - - +
57A GLN* 1.3 61.8 + - - +
58A LEU* 3.7 17.4 + - + -
160A PHE* 4.7 5.2 - - + +
163A ILE* 6.2 0.4 - - + -
164A ILE* 3.2 40.2 - - + -
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Residues in contact with GLN 57 (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 2.7 14.4 + - - +
8A LYS* 3.0 42.3 + - + +
9A ILE 2.8 25.1 + - - -
42A THR* 4.3 21.9 - - + +
43A PHE 3.8 2.5 - - - -
44A THR* 4.4 14.6 + - + +
55A HIS 3.7 1.7 + - - +
56A LEU* 1.3 72.0 - - - +
58A LEU* 1.3 61.4 + - - +
59A VAL* 5.1 1.6 - - + -
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Residues in contact with LEU 58 (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* 3.3 28.0 - - + -
11A ILE* 4.1 7.4 - - + -
23A THR* 4.3 11.4 - - + -
26A PHE* 3.7 33.4 - - + -
27A VAL* 3.9 17.0 - - + -
41A ASN 3.9 0.2 - - - +
42A THR* 3.3 9.5 + - - +
43A PHE* 3.0 36.3 + - + +
45A LYS* 4.6 2.9 - - + -
56A LEU* 4.3 20.4 - - + +
57A GLN* 1.3 74.7 - - - +
59A VAL* 1.3 61.2 + - - +
60A ASP 3.9 0.6 + - - -
160A PHE* 3.7 26.9 - - + -
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Residues in contact with VAL 59 (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 LYS* 3.9 29.8 - - + +
9A ILE 2.7 17.6 + - - +
10A ALA* 3.6 7.1 - - + -
11A ILE* 3.0 26.5 + - - +
40A GLU* 3.7 34.3 - - + +
41A ASN 3.7 5.2 - - - +
42A THR* 4.2 9.0 - - - +
57A GLN* 4.4 3.1 - - + +
58A LEU* 1.3 75.2 - - - +
60A ASP* 1.3 59.2 + - - +
61A THR* 3.2 7.5 + - + +
74A TYR* 3.9 16.8 - - + +
78A ILE* 4.9 5.2 - - + -
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Residues in contact with ASP 60 (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 ILE* 4.4 7.2 - - - +
19A LYS* 3.4 26.0 - - - +
20A SER* 2.5 41.0 + - - -
23A THR* 4.3 18.3 + - + +
24A ILE* 4.9 0.3 - - - +
38A THR* 3.7 1.9 + - - +
40A GLU* 3.6 5.4 - - - -
41A ASN* 3.0 51.9 + - + +
43A PHE* 4.5 4.1 - - + -
58A LEU 3.9 2.2 + - - -
59A VAL* 1.3 68.0 - - - +
61A THR* 1.3 61.8 + - - +
178A MG 3.6 6.1 - - - -
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Residues in contact with THR 61 (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* 4.7 1.8 - - + -
11A ILE 2.7 22.0 + - - +
12A LEU* 3.4 28.9 - - + +
13A GLY 4.6 0.5 + - - -
19A LYS* 3.3 17.0 - - - -
38A THR* 4.5 1.1 - - - -
40A GLU* 4.6 1.1 - - - -
59A VAL* 3.2 13.8 + - + +
60A ASP* 1.3 77.8 + - - +
62A ALA* 1.3 69.8 + - - +
63A GLY 3.7 0.2 + - - -
64A GLN* 4.9 1.0 + - - +
74A TYR* 3.3 48.0 - - + +
178A MG 4.0 5.4 - - - -
180A GOL 4.5 1.1 - - - -
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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