Contacts of the helix formed by residues 3 - 16 (chain A) in PDB entry 1UR6
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 LEU 3 (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* 4.6 1.9 - - + +
2A ALA* 1.3 74.9 - - - +
4A LYS* 1.3 65.5 + - - +
5A ARG 3.0 3.1 - - - -
6A ILE* 2.9 40.2 + - + +
7A HIS* 3.9 2.1 + - - +
30A MET* 5.3 9.9 - - + -
31A PHE* 3.5 35.4 - - + -
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Residues in contact with LYS 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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1A MET 5.0 1.4 - - - +
2A ALA 3.2 1.0 - - - +
3A LEU* 1.3 77.8 - - - +
5A ARG* 1.3 51.1 + - - +
7A HIS* 3.2 9.0 + - + +
8A LYS* 2.7 49.8 + - + +
13B GLU* 2.7 29.0 + - - -
18B MET 2.7 21.6 + - - +
19B GLU* 2.7 47.6 + - + +
20B PRO* 3.6 4.0 - - - +
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Residues in contact with ARG 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 ALA 3.5 13.7 - - - +
3A LEU 2.9 0.2 + - - -
4A LYS* 1.3 76.2 - - - +
6A ILE* 1.3 57.4 + - - +
9A GLU* 2.8 63.7 + - - +
60A TYR* 3.6 24.7 + - + -
61A PRO* 3.7 26.7 - - - +
96A ALA* 3.8 4.9 + - - +
97A LEU 2.8 31.5 + - - +
98A THR* 3.2 24.7 - - - +
15B PRO* 2.7 29.7 + - - +
16B LEU 3.5 7.5 + - - -
17B CYS 3.1 16.3 + - - +
18B MET* 3.4 23.8 - - + +
35B TYR* 5.7 0.2 + - - -
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Residues in contact with ILE 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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2A ALA 4.3 3.8 - - - +
3A LEU* 2.9 44.1 + - + +
5A ARG* 1.3 76.4 - - - +
7A HIS* 1.3 60.7 + - + +
9A GLU* 4.1 0.8 - - - -
10A LEU* 3.1 27.3 + - + +
26A VAL* 5.9 1.6 - - + -
30A MET* 3.2 37.0 - - + +
31A PHE* 4.0 13.7 - - + -
33A TRP* 3.4 18.9 + - + +
56A PHE* 3.7 22.0 - - + -
60A TYR* 3.5 26.5 - - + -
61A PRO* 5.6 0.2 - - + -
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Residues in contact with HIS 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 LEU 3.9 1.3 + - - +
4A LYS* 3.2 12.0 + - + +
6A ILE* 1.3 79.1 - - + +
8A LYS* 1.3 65.8 + - - +
10A LEU* 3.3 27.1 - - + +
11A ASN* 2.9 25.8 + - - +
26A VAL* 5.2 0.2 - - - +
30A MET* 3.9 34.5 - - + +
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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
----------------------------------------------------------
4A LYS* 2.7 47.9 + - + +
5A ARG 3.8 0.4 - - - +
7A HIS* 1.3 74.0 - - - +
9A GLU* 1.3 58.4 + - - +
11A ASN* 3.5 3.8 + - - +
12A ASP* 2.9 36.9 + - + +
15A ARG* 4.9 6.1 + - - +
13B GLU* 2.6 29.6 + - - +
18B MET* 3.6 32.3 + - + +
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Residues in contact with GLU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 2.8 42.0 + - + +
6A ILE* 4.3 0.7 - - - +
8A LYS* 1.3 69.7 - - - +
10A LEU* 1.3 60.2 + - - +
12A ASP* 3.8 7.4 - - + -
13A LEU* 2.9 36.9 + - + +
33A TRP* 3.5 6.8 - - + -
60A TYR* 2.6 28.9 + - - +
98A THR* 2.6 30.5 + - - -
99A ILE* 2.9 23.5 + - + +
100A SER* 4.3 0.7 + - - -
18B MET* 3.6 26.3 - - + +
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Residues in contact with LEU 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 ILE 3.1 19.8 + - - +
7A HIS* 3.2 29.1 + - + +
9A GLU* 1.3 77.1 - - - +
11A ASN* 1.3 60.6 + - + +
14A ALA* 3.1 24.1 + - + +
23A ALA* 3.6 6.8 - - + +
24A GLY 3.3 35.8 + - - +
25A PRO 3.8 14.1 - - - +
26A VAL* 3.7 25.8 - - + -
33A TRP* 3.2 35.4 - - + +
34A GLN 6.3 0.2 - - - -
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A HIS 2.9 15.5 + - - +
8A LYS* 4.1 3.6 - - - +
10A LEU* 1.3 77.5 - - + +
12A ASP* 1.3 65.8 + - - +
14A ALA* 3.0 16.4 + - - +
15A ARG* 2.9 62.9 + - - +
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Residues in contact with ASP 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 LYS* 2.9 27.1 + - - +
9A GLU* 3.5 10.8 - - - +
11A ASN* 1.3 78.3 - - - +
13A LEU* 1.3 68.1 + - + +
14A ALA 3.2 3.6 + - - -
15A ARG* 3.0 29.3 + - - +
16A ASP* 3.2 37.1 + - - +
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Residues in contact with LEU 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 GLU* 2.9 27.0 + - + +
12A ASP* 1.3 89.4 - - + +
14A ALA* 1.3 57.5 + - - +
16A ASP 4.1 0.9 - - - +
17A PRO* 3.2 22.5 - - - +
18A PRO* 3.6 30.1 - - + -
21A CYS 5.0 1.3 - - - +
23A ALA* 2.8 37.8 + - + +
33A TRP* 4.2 0.9 - - + -
99A ILE* 4.1 16.4 - - + -
100A SER* 3.6 24.5 - - - +
103A LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 14 (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 LEU 3.1 18.3 + - - +
11A ASN* 3.0 14.1 + - - +
13A LEU* 1.3 79.9 - - - +
15A ARG* 1.3 68.8 + - + +
17A PRO* 3.7 9.4 - - - +
23A ALA 3.5 18.1 - - - +
24A GLY* 3.7 11.4 - - - +
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Residues in contact with ARG 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LYS* 4.9 6.5 + - - +
11A ASN* 2.9 41.5 + - - +
12A ASP* 3.0 44.3 + - - +
14A ALA* 1.3 78.6 - - + +
16A ASP* 1.3 79.6 + - + +
17A PRO* 3.2 8.8 - - - +
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Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASP* 3.2 21.0 + - - +
13A LEU* 4.1 1.6 - - - +
15A ARG* 1.3 112.7 + - + +
17A PRO* 1.3 64.2 - - - +
18A PRO* 3.9 1.7 - - - +
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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