Contacts of the helix formed by residues 7 - 22 (chain A) in PDB entry 1UWY
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 ARG 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A TYR* 5.3 6.3 - - + +
6A HIS* 1.3 85.4 - - - +
8A GLN* 1.3 67.0 + - - +
9A GLU* 3.4 5.1 + - + +
10A GLY* 3.6 3.3 + - - +
11A MET* 3.0 13.2 + - - +
73A ARG* 3.7 2.7 - - - -
113A PHE* 3.3 45.5 + - + -
114A GLU* 3.2 47.2 + - - +
116A VAL 3.5 10.8 + - - -
117A LYS* 3.8 22.6 - - - +
270A TYR* 4.6 3.8 + - - -
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Residues in contact with GLN 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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7A ARG* 1.3 72.1 - - - +
9A GLU* 1.3 93.7 + - + +
11A MET* 4.6 10.4 - - + +
12A GLU* 2.9 48.8 + - - +
38A ARG* 2.7 42.6 + - - +
39A ASN 5.7 1.1 - - - +
41A TRP* 5.6 0.9 - - - +
73A ARG* 5.1 0.2 - - - +
110A PRO* 5.9 2.0 - - + -
114A GLU* 3.3 26.0 + - - +
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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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7A ARG* 3.4 3.4 + - + +
8A GLN* 1.3 104.0 + - + +
10A GLY* 1.3 54.6 + - - +
12A GLU* 3.2 7.7 - - - +
13A ALA* 2.7 32.1 + - - +
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Residues in contact with GLY 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 HIS* 4.4 15.7 - - - -
7A ARG 3.6 4.3 + - - +
8A GLN 3.5 0.2 - - - -
9A GLU* 1.3 77.9 - - - +
11A MET* 1.3 59.0 + - - +
13A ALA* 3.2 8.7 - - - +
14A PHE* 2.9 27.5 + - - +
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Residues in contact with MET 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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6A HIS* 3.3 24.4 - - + +
7A ARG 3.0 8.8 + - - +
8A GLN* 4.6 7.2 - - + +
10A GLY* 1.3 72.6 - - - +
12A GLU* 1.3 68.4 + - - +
14A PHE* 3.1 7.7 + - - +
15A LEU* 2.9 48.6 + - - +
41A TRP* 5.1 8.1 - - + -
73A ARG* 3.0 40.6 - - - +
77A LEU* 3.3 34.1 - - + -
106A PRO* 3.8 18.6 - - + -
107A SER* 4.3 9.6 - - - -
110A PRO* 5.6 1.6 - - + -
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Residues in contact with GLU 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 GLN* 2.9 49.9 + - - +
9A GLU* 3.2 7.7 - - - +
11A MET* 1.3 80.5 - - - +
13A ALA* 1.3 69.2 + - - +
15A LEU* 3.1 12.1 + - - +
16A LYS* 2.9 34.8 + - + +
28A LEU* 6.5 0.2 - - + -
39A ASN* 4.0 5.7 + - - +
41A TRP* 2.7 52.8 + - + +
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Residues in contact with ALA 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 2.7 17.3 + - - +
10A GLY* 3.2 16.2 - - - +
12A GLU* 1.3 75.5 - - - +
14A PHE* 1.3 67.1 + - - +
16A LYS* 2.9 19.9 + - - +
17A THR* 2.9 18.3 + - - +
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Residues in contact with PHE 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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1A LEU* 3.6 35.7 - - + -
6A HIS* 5.4 0.9 - - + -
10A GLY 2.9 11.8 + - - +
11A MET* 3.2 11.0 - - - +
13A ALA* 1.3 75.2 - - - +
15A LEU* 1.3 66.3 + - + +
17A THR* 3.0 9.4 + - - -
18A VAL* 2.6 58.6 + - + +
77A LEU* 3.8 36.1 - - + -
80A ILE* 3.2 32.8 - - + -
81A ASP* 3.9 25.4 - - + -
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Residues in contact with LEU 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 MET* 2.9 44.8 + - - +
12A GLU* 3.1 11.2 - - - +
13A ALA 3.0 0.2 + - - -
14A PHE* 1.3 86.4 - - + +
16A LYS* 1.3 56.5 + - - +
18A VAL* 2.6 30.0 + - - +
19A ALA* 2.7 10.6 + - - +
28A LEU* 4.2 19.1 - - + -
41A TRP* 4.3 20.2 - - + -
42A VAL 5.7 0.2 - - - -
43A LEU* 3.8 30.6 - - + +
77A LEU* 4.2 8.7 - - + -
80A ILE* 3.9 16.2 - - + -
106A PRO* 4.6 8.5 - - + -
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Residues in contact with LYS 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 GLU* 2.9 33.9 + - + +
13A ALA* 2.9 13.9 + - - +
15A LEU* 1.3 74.7 - - - +
17A THR* 1.3 58.6 + - - +
19A ALA* 2.6 28.8 - - - +
20A GLN* 3.0 14.8 + - - +
28A LEU* 3.8 13.5 - - + +
41A TRP* 3.8 23.7 - - - -
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Residues in contact with THR 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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13A ALA* 2.9 17.7 + - - +
14A PHE* 3.3 10.4 - - - -
16A LYS* 1.3 72.8 - - - +
18A VAL* 1.3 62.8 + - - +
19A ALA 2.9 4.3 - - - -
20A GLN* 2.9 18.5 + - + +
21A ASN* 3.0 30.7 + - + +
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Residues in contact with VAL 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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14A PHE* 2.6 58.2 + - + +
15A LEU* 2.6 11.6 + - - +
17A THR* 1.3 71.2 - - + +
19A ALA* 1.3 61.8 + - - +
21A ASN* 4.9 1.1 - - - -
22A TYR* 3.1 34.2 + - + +
26A THR* 3.5 7.1 + - + -
43A LEU* 4.1 18.6 - - + -
80A ILE* 4.4 3.6 - - + -
84A VAL* 3.8 33.9 - - + -
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Residues in contact with ALA 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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15A LEU 2.7 7.1 + - - +
16A LYS* 2.6 26.0 - - - +
18A VAL* 1.3 77.2 - - - +
20A GLN* 1.3 60.8 + - + +
23A SER* 3.1 32.7 + - - -
26A THR* 3.8 9.3 + - - +
27A HIS* 6.1 0.4 - - - +
28A LEU* 4.6 20.6 - - + +
43A LEU* 5.4 1.7 - - - +
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Residues in contact with GLN 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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16A LYS* 3.4 15.7 - - + +
17A THR* 2.9 9.7 + - + +
19A ALA* 1.3 76.0 + - - +
21A ASN* 1.3 64.1 + - - +
22A TYR 2.8 10.6 + - - -
23A SER* 3.2 20.3 + - - -
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Residues in contact with ASN 21 (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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17A THR* 3.0 28.6 + - + +
18A VAL* 4.9 0.2 - - - -
20A GLN* 1.3 79.6 - - - +
22A TYR* 1.3 86.5 + - + +
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Residues in contact with TYR 22 (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 VAL* 3.1 24.6 + - + +
20A GLN 2.8 5.7 + - - -
21A ASN* 1.3 100.2 + - + +
23A SER* 1.3 51.1 + - - +
24A SER* 2.6 20.1 + - - -
25A VAL* 2.8 21.3 + - + +
26A THR* 3.4 23.4 + - + +
84A VAL* 3.7 42.0 - - + -
85A THR* 3.5 25.4 - - + +
87A ASP* 6.3 0.2 - - + -
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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