Contacts of the strand formed by residues 14 - 20 (chain A) in PDB entry 1J71
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 TYR 14 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A LEU* 4.5 19.7 - - + -
8A ILE 3.4 6.5 - - - +
9A ASN* 3.4 47.7 + - + -
11A GLY 5.2 2.2 - - - -
13A SER* 1.3 82.3 - - - +
15A ALA* 1.3 60.2 + - - +
30A VAL* 3.4 8.5 - - - +
31A ILE* 2.9 29.5 + - + +
160A LEU* 3.4 54.0 + - + -
162A SER 4.7 0.3 + - - -
168A GLY 5.4 1.8 - - - -
219A SER* 5.1 6.2 + - - +
301A ASP* 3.8 24.7 - - - -
305A ARG* 3.0 40.1 + - - +
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Residues in contact with ALA 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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7A LEU* 3.2 6.8 - - - -
8A ILE* 2.7 41.3 + - + +
10A GLU* 3.3 31.4 - - + +
14A TYR* 1.3 75.5 - - - +
16A ALA* 1.3 59.7 + - - +
28A THR* 3.6 11.0 - - + -
29A VAL 3.0 25.6 - - - +
30A VAL* 4.0 1.8 - - - +
31A ILE* 4.2 3.4 - - - +
121A GLN* 4.1 0.7 - - - +
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Residues in contact with ALA 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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5A THR* 4.0 18.2 - - + -
6A THR 3.8 15.5 - - - +
7A LEU* 4.5 0.7 - - + -
8A ILE* 5.5 1.6 - - - -
15A ALA* 1.3 75.5 - - - +
17A ASP* 1.3 67.7 + - - +
18A ILE* 3.7 8.3 + - + -
28A THR* 3.4 2.3 - - - -
29A VAL* 2.8 33.0 + - + +
31A ILE* 3.8 25.7 - - + +
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Residues in contact with ASP 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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5A THR* 5.4 2.3 - - - +
6A THR 4.8 1.6 + - - -
8A ILE* 3.7 22.7 - - - +
16A ALA* 1.3 74.7 - - - +
18A ILE* 1.3 63.6 + - - +
26A LYS* 6.5 1.6 - - + -
27A GLN 3.4 4.3 - - - +
28A THR* 2.7 33.4 + - - +
101A PHE* 3.9 12.8 - - - +
102A GLY 5.1 0.9 + - - -
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Residues in contact with ILE 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 ALA* 4.2 7.4 - - + +
17A ASP* 1.3 79.6 - - - +
19A VAL* 1.3 66.7 + - - +
20A VAL* 4.0 19.5 - - + -
26A LYS* 3.4 5.0 - - - +
27A GLN* 2.8 48.2 + - + +
29A VAL* 4.0 32.3 - - + -
38A LEU* 4.3 15.5 - - + -
40A VAL* 4.6 2.5 - - + -
99A VAL* 4.5 9.6 - - + -
100A GLY 3.3 10.5 - - - +
101A PHE* 3.9 15.9 - - + -
124A MET* 4.0 18.6 - - + -
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Residues in contact with VAL 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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18A ILE* 1.3 78.8 - - - +
20A VAL* 1.3 65.2 + - - +
24A GLN* 3.7 49.6 - - + +
25A GLN 3.3 4.3 - - - -
26A LYS* 4.0 17.7 - - + -
98A THR 3.9 0.3 - - - +
99A VAL* 3.4 4.3 - - - +
100A GLY* 2.8 54.5 + - - +
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Residues in contact with VAL 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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18A ILE* 4.0 23.1 - - + -
19A VAL* 1.3 81.1 - - - +
21A GLY* 1.3 66.4 + - - +
25A GLN* 2.9 37.1 + - - +
27A GLN* 4.1 13.5 - - + -
38A LEU* 5.9 0.4 - - + -
40A VAL* 4.4 8.7 - - + -
65A PHE* 3.6 23.0 - - + -
97A ASP* 4.5 0.9 - - + -
98A THR 3.4 8.3 - - - +
99A VAL* 4.5 8.7 - - + -
111A PHE* 3.6 37.0 - - + -
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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