Contacts of the helix formed by residues 6 - 16 (chain A) in PDB entry 1U5U
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 PHE 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LYS* 3.3 57.0 - - + +
5A ASN* 1.3 71.5 - - - +
7A GLY* 1.3 64.2 + - - +
8A PHE 3.4 2.7 - - - -
9A GLU* 3.2 26.5 + - + +
10A ILE* 2.8 41.7 + - + +
232A GLU* 3.5 53.8 - - + -
235A GLN* 2.7 20.0 + - - +
236A ARG* 4.3 8.5 - - - +
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Residues in contact with GLY 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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5A ASN* 2.7 17.0 + - - -
6A PHE* 1.3 76.4 - - - +
8A PHE* 1.3 64.1 - - - +
10A ILE* 3.5 2.5 + - - +
11A PHE* 3.1 22.3 + - - +
173A TYR* 3.8 33.4 - - - +
174A TYR* 4.0 9.2 - - - -
177A VAL* 4.6 0.2 - - - -
235A GLN* 4.0 2.4 + - - -
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Residues in contact with PHE 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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5A ASN 5.1 0.8 + - - +
6A PHE 3.4 0.4 - - - -
7A GLY* 1.3 71.5 - - - +
9A GLU* 1.3 63.0 + - + +
11A PHE* 3.2 4.0 + - - +
12A GLY 2.8 25.6 + - - -
20A LEU* 3.6 23.5 - - + +
24A ILE* 4.0 18.8 - - + -
170A PRO* 3.3 44.6 - - + -
171A TYR* 3.8 33.0 - + - -
174A TYR* 3.5 39.5 - + + -
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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
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4A LYS* 2.6 41.5 + - - -
5A ASN 5.6 1.1 + - - +
6A PHE* 3.2 26.5 + - + +
8A PHE* 1.3 78.2 - - + +
10A ILE* 1.3 57.7 + - + +
12A GLY* 3.2 2.2 + - - -
13A GLU* 2.8 44.9 + - + +
20A LEU* 5.2 2.0 - - - -
236A ARG* 5.3 1.1 + - - +
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Residues in contact with ILE 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 PHE* 2.8 37.4 + - + +
7A GLY 3.8 4.0 - - - +
9A GLU* 1.3 72.6 - - - +
11A PHE* 1.3 65.6 + - - +
13A GLU* 3.3 17.8 + - - +
14A LYS* 3.3 9.2 + - - +
167A TYR* 3.3 28.1 + - + +
173A TYR* 3.4 42.4 - - + +
235A GLN* 4.0 8.3 - - + +
236A ARG* 3.8 42.0 - - + +
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Residues in contact with PHE 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 GLY 3.1 14.3 + - - +
8A PHE 3.2 8.3 + - - +
10A ILE* 1.3 75.4 - - - +
12A GLY* 1.3 59.1 + - - +
14A LYS* 3.2 2.1 + - - -
15A TYR* 3.0 53.7 + + + +
19A GLU* 4.4 2.9 - - + -
20A LEU* 3.7 37.5 - - + -
23A ARG* 4.0 21.5 - - + -
166A VAL 4.4 2.5 - - - -
167A TYR* 3.3 44.4 - + - -
169A ASN 3.9 2.9 - - - -
170A PRO* 3.7 45.3 - - + -
173A TYR* 4.9 3.5 - - + -
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Residues in contact with GLY 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 PHE 2.8 14.7 + - - -
9A GLU* 3.6 3.6 - - - -
11A PHE* 1.3 76.8 - - - +
13A GLU* 1.3 60.2 + - - +
16A GLY* 2.7 46.3 + - - -
17A GLN* 4.1 2.9 + - - -
20A LEU* 4.3 14.4 - - - -
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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 GLU* 2.8 28.4 + - + +
10A ILE* 3.5 11.5 - - - +
11A PHE 3.3 0.6 - - - -
12A GLY* 1.3 76.6 - - - +
14A LYS* 1.3 59.5 + - - +
16A GLY 4.8 0.5 + - - -
236A ARG* 2.9 42.3 + - - -
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Residues in contact with LYS 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 ILE 3.3 2.1 + - - +
11A PHE 3.2 7.9 + - - +
12A GLY 3.1 0.4 - - - -
13A GLU* 1.3 82.1 - - - +
15A TYR* 1.3 96.7 + - + +
164A GLU* 6.3 0.2 - - - +
167A TYR* 3.4 54.4 - - + +
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Residues in contact with TYR 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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11A PHE* 3.0 39.8 + + + +
14A LYS* 1.3 122.2 + - + +
16A GLY* 1.3 58.7 + - - +
19A GLU* 3.5 34.3 + - + +
167A TYR* 3.3 33.3 + + - +
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Residues in contact with GLY 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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12A GLY* 2.7 25.9 + - - +
13A GLU 4.6 0.2 - - - -
14A LYS 3.7 1.0 - - - -
15A TYR* 1.3 74.2 - - - +
17A GLN* 1.3 66.6 + - - -
18A GLU* 3.3 3.1 - - - -
19A GLU 3.3 2.7 + - - -
20A LEU* 3.0 21.7 + - - +
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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