Contacts of the helix formed by residues 2 - 13 (chain A) in PDB entry 1UJP
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 THR 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 77.4 - - - +
3A THR* 1.3 64.6 + - - +
4A LEU* 3.6 7.8 + - - +
5A GLU* 2.9 41.8 + - - +
6A ALA* 2.9 21.5 + - - +
93A PRO* 3.8 0.4 - - - -
121A THR* 5.9 2.7 - - - -
146A GLU* 5.9 1.1 - - - -
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Residues in contact with THR 3 (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 THR* 1.3 73.4 - - - +
4A LEU* 1.3 62.7 + - - +
6A ALA* 3.2 3.9 + - - +
7A PHE* 3.1 44.3 + - + -
45A LEU* 3.7 9.2 - - + -
93A PRO* 3.8 11.5 - - - +
95A PHE* 3.4 13.8 - - + -
121A THR* 3.6 8.5 - - - +
146A GLU* 2.5 31.6 + - - +
169A GLY* 3.5 31.4 - - - +
170A PHE* 4.1 4.3 - - + -
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Residues in contact with LEU 4 (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 THR* 3.3 7.5 + - - +
3A THR* 1.3 81.5 - - - +
5A GLU* 1.3 58.3 + - + +
7A PHE* 3.3 5.6 + - + +
8A ALA* 2.9 34.4 + - + +
146A GLU* 5.2 1.2 + - - -
169A GLY 5.3 1.5 + - - +
204A PRO* 4.3 24.0 - - + -
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Residues in contact with GLU 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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1A MET* 3.4 23.0 + - - +
2A THR* 2.9 46.8 + - - +
4A LEU* 1.3 79.6 - - + +
6A ALA* 1.3 57.7 + - - +
8A ALA* 3.7 6.9 - - - +
9A LYS* 2.9 30.8 + - - +
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Residues in contact with ALA 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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1A MET* 3.7 14.5 - - + -
2A THR 2.9 12.8 + - - +
3A THR 3.2 8.7 + - - +
5A GLU* 1.3 77.7 - - - +
7A PHE* 1.3 63.0 + - - +
9A LYS* 3.5 4.9 + - - +
10A ALA* 3.3 20.1 + - - +
44A ASP* 3.5 33.6 - - + +
45A LEU* 3.9 15.7 - - + -
93A PRO* 4.0 5.8 - - + -
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Residues in contact with PHE 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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3A THR* 3.1 32.5 + - + -
4A LEU* 3.8 6.1 - - + +
6A ALA* 1.3 78.6 - - - +
8A ALA* 1.3 63.7 + - - +
10A ALA* 3.3 7.0 + - - +
11A ARG* 3.0 22.5 + - - +
17A ALA* 4.1 7.0 - - + -
19A ILE* 4.0 17.7 - - + -
45A LEU* 3.6 20.9 - - + -
170A PHE* 3.8 32.1 - + + -
204A PRO* 3.6 31.4 - - + -
205A VAL 5.0 0.4 - - - -
206A ALA* 4.6 3.4 - - + -
224A ASP* 3.5 33.7 - - + +
225A GLY* 3.9 15.5 - - - -
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Residues in contact with ALA 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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4A LEU* 2.9 21.7 + - + +
5A GLU* 3.7 8.7 - - - +
7A PHE* 1.3 77.4 - - - +
9A LYS* 1.3 57.7 + - - +
11A ARG* 3.2 7.0 + - - +
12A SER* 2.9 31.1 + - - -
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Residues in contact with LYS 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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1A MET* 3.8 25.8 - - + -
5A GLU 2.9 17.9 + - - +
6A ALA* 3.7 6.3 - - - +
7A PHE 3.3 0.2 - - - -
8A ALA* 1.3 75.8 - - - +
10A ALA* 1.3 63.2 + - - +
12A SER* 2.8 23.1 + - - +
13A GLU* 2.7 48.2 + - - +
15A ARG* 4.7 7.1 - - - +
44A ASP* 5.7 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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6A ALA 3.3 6.4 + - - +
7A PHE 3.3 8.6 + - - +
8A ALA 3.3 0.4 - - - -
9A LYS* 1.3 79.1 - - - +
11A ARG* 1.3 62.6 + - - +
13A GLU 3.0 9.7 + - - -
14A GLY 3.2 0.2 + - - -
15A ARG* 3.1 58.6 + - - +
17A ALA* 3.8 31.6 - - + +
44A ASP* 4.5 0.7 - - - +
224A ASP 5.0 0.9 - - - +
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Residues in contact with ARG 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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7A PHE 3.0 14.0 + - - +
8A ALA* 3.6 9.9 - - - +
10A ALA* 1.3 77.6 - - - +
12A SER* 1.3 58.1 + - - +
14A GLY* 2.8 19.9 + - - -
15A ARG 3.7 6.5 + - - -
198A LYS* 4.5 9.1 - - - +
222A VAL 4.5 4.4 + - - -
224A ASP* 2.8 29.7 + - - +
255A ARG* 3.4 39.7 + - - +
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Residues in contact with SER 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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8A ALA 2.9 15.0 + - - -
9A LYS* 2.8 24.7 + - - +
11A ARG* 1.3 77.6 - - - +
13A GLU* 1.3 61.9 + - - +
14A GLY 3.2 1.0 + - - -
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Residues in contact with GLU 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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9A LYS* 2.7 44.1 + - - +
10A ALA 3.0 8.8 + - - +
12A SER* 1.3 81.3 - - - +
14A GLY* 1.3 57.5 - - - +
15A ARG* 2.7 44.5 + - - +
254A GLN* 3.0 20.8 + - - +
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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