Contacts of the helix formed by residues 2 - 8 (chain A) in PDB entry 3UR9
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 PRO 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A MET* 3.4 8.7 - - + +
1A ALA* 1.3 86.9 - - - +
3A PRO* 1.3 78.6 - - + +
4A THR* 4.4 5.4 - - - +
5A LEU* 3.0 30.2 + - + +
6A TRP* 3.2 11.3 + - - -
151A TRP* 3.7 25.4 - - + +
3B PRO* 4.1 0.9 - - + -
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Residues in contact with PRO 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 PRO* 1.3 87.2 - - + +
4A THR* 1.3 57.6 + - - +
6A TRP* 3.1 9.9 + - + +
7A SER 2.9 23.6 + - - -
1B ALA 3.6 23.6 - - - +
3B PRO* 3.8 24.4 - - + -
6B TRP* 3.7 16.8 - - + +
94B LEU* 3.6 28.1 - - + +
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Residues in contact with THR 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 PRO* 3.3 6.9 - - - +
3A PRO* 1.3 77.2 - - - +
5A LEU* 1.3 62.9 + - - +
7A SER* 2.7 25.7 + - - +
8A ARG* 3.5 17.4 + - - +
67A ASP* 5.8 1.8 - - - +
68A LEU* 4.0 21.1 - - + -
69A THR 6.2 0.2 - - - +
94B LEU* 4.3 6.7 - - - +
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Residues in contact with LEU 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 ALA* 3.7 21.8 - - + -
2A PRO* 3.0 21.5 + - + +
4A THR* 1.3 76.9 - - - +
6A TRP* 1.3 65.3 + - - +
8A ARG* 3.1 31.1 + - - +
9A VAL* 4.0 2.3 + - - +
18A PHE* 3.9 28.4 - - + -
71A MET* 4.0 17.0 - - + -
86A LEU* 3.7 16.2 - - + -
144A VAL* 4.3 3.6 - - + -
151A TRP* 3.6 42.4 - - + -
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Residues in contact with TRP 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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0A MET* 5.7 1.2 - - - +
1A ALA* 3.6 21.5 + - + +
2A PRO 3.2 18.7 + - - -
3A PRO* 3.1 8.6 + - + +
5A LEU* 1.3 77.8 - - - +
7A SER* 1.3 58.0 + - - +
8A ARG 3.0 0.2 - - - -
9A VAL* 3.0 22.0 + - + +
86A LEU* 3.5 52.7 - - + -
87A ILE 3.5 21.5 - - - -
88A LYS* 3.2 30.4 + - + -
94A LEU* 3.7 32.5 - - + +
96A PRO* 3.8 35.0 - - + -
201A CL 3.8 11.4 - - + -
3B PRO* 3.7 25.0 - - + +
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Residues in contact with SER 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 PRO 2.9 12.7 + - - -
4A THR* 2.7 21.9 + - - +
5A LEU 3.1 1.0 - - - -
6A TRP* 1.3 76.6 - - - +
8A ARG* 1.3 58.3 + - - +
9A VAL 3.3 5.1 + - - +
10A THR* 4.3 1.6 + - - -
65A ARG* 2.9 37.2 + - - -
67A ASP* 4.7 0.7 + - - -
68A LEU* 4.2 3.1 - - - +
88A LYS* 4.5 1.0 + - - +
201A CL 3.6 10.5 - - - -
92B GLY* 3.4 25.2 - - - +
94B LEU* 3.7 19.8 + - - +
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Residues in contact with ARG 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 THR* 3.5 19.5 + - - +
5A LEU* 3.2 18.2 - - - +
6A TRP 3.0 0.6 - - - -
7A SER* 1.3 77.7 - - - +
9A VAL* 1.3 56.7 + - - +
10A THR* 3.0 14.6 + - - -
18A PHE* 3.3 30.8 - - + -
19A TRP* 3.0 52.2 + - - +
20A VAL 3.1 21.4 + - - -
65A ARG* 4.4 4.9 - - - +
68A LEU* 3.9 28.5 - - + +
69A THR* 2.8 41.8 + - - +
71A MET* 3.7 19.2 - - - +
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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