Contacts of the helix formed by residues 5 - 16 (chain A) in PDB entry 1UK0
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 5 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A LYS 4.6 1.3 - - - +
4A LEU* 1.4 109.0 - - + +
6A LYS* 1.3 64.9 + - - +
7A PRO 4.0 0.2 - - - -
8A VAL* 3.7 12.1 + - + -
9A GLN* 3.0 18.5 + - - +
140A ILE 4.9 4.5 - - - +
142A VAL* 4.2 22.0 - - + +
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Residues in contact with LYS 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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4A LEU 4.8 0.7 - - - +
5A PRO* 1.3 80.8 - - - +
7A PRO* 1.4 65.6 - - + +
9A GLN* 3.2 20.3 + - + +
10A ASP* 2.8 45.0 + - - +
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Residues in contact with PRO 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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6A LYS* 1.4 92.4 - - + +
8A VAL* 1.4 69.5 + - - +
10A ASP* 3.5 11.9 - - + +
11A LEU* 2.7 25.1 + - - +
142A VAL* 4.2 23.3 - - + -
174A ASP* 2.9 42.2 - - - +
176A PHE* 3.5 11.2 - - + -
343A LYS* 4.9 2.0 - - - +
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Residues in contact with VAL 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* 3.9 18.6 - - + -
5A PRO* 3.7 14.1 + - + +
6A LYS 3.3 1.4 - - - -
7A PRO* 1.4 85.6 - - - +
9A GLN* 1.3 62.4 + - - +
11A LEU* 3.3 4.3 - - + +
12A ILE* 2.9 28.0 + - + +
133A TYR* 3.9 31.2 - - + -
140A ILE* 3.5 30.5 - - + +
142A VAL* 4.1 8.5 - - + +
176A PHE* 3.4 22.4 - - + -
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Residues in contact with GLN 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 LYS* 4.0 11.6 + - - +
2A SER* 3.0 38.2 + - - -
4A LEU* 2.6 29.3 + - + +
5A PRO 3.0 13.4 - - - +
6A LYS* 3.2 17.8 + - + +
8A VAL* 1.3 74.9 - - - +
10A ASP* 1.3 65.5 + - - +
12A ILE* 3.6 2.3 + - - +
13A LYS* 3.2 33.9 + - - +
129A ILE* 3.7 24.6 - - + +
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Residues in contact with ASP 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 LYS* 2.8 41.0 - - - +
7A PRO* 3.1 7.9 + - - +
9A GLN* 1.3 76.8 - - - +
11A LEU* 1.4 53.2 - - - +
13A LYS* 2.4 39.5 + - - +
14A MET* 2.6 36.6 + - - +
343A LYS* 4.1 20.6 + - - +
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Residues in contact with LEU 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 PRO 2.7 21.5 + - - +
8A VAL* 3.3 7.6 - - + +
10A ASP* 1.4 66.7 - - - +
12A ILE* 1.4 73.6 + - + +
14A MET* 3.2 11.5 + - + +
15A ILE* 2.7 50.7 + - + +
140A ILE* 3.8 38.4 - - + -
176A PHE* 4.0 18.6 - - + -
257A LEU* 3.6 30.7 - - + -
341A LEU* 3.9 15.0 - - + -
343A LYS* 5.1 3.3 - - + +
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Residues in contact with ILE 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 VAL* 2.9 32.0 + - + +
9A GLN 3.9 2.2 - - - +
11A LEU* 1.4 80.5 - - + +
13A LYS* 1.4 53.2 + - - +
14A MET 2.7 10.2 + - - -
15A ILE* 2.8 12.0 + - - -
16A PHE* 2.9 25.2 + - + -
128A PRO 4.7 2.2 - - - +
129A ILE* 3.5 31.9 - - + +
132A ASN* 3.6 19.5 - - + +
133A TYR* 3.4 57.0 - - + +
136A LEU* 4.1 9.0 - - + -
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Residues in contact with LYS 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 GLN* 3.2 27.1 + - - +
10A ASP* 2.4 41.7 + - - +
12A ILE* 1.4 72.0 - - - +
14A MET* 1.4 55.9 + - - +
16A PHE* 4.8 3.4 - - - +
17A ASP* 3.1 30.4 - - - +
129A ILE* 4.0 20.6 - - + +
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Residues in contact with MET 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 ASP* 2.6 18.9 + - + +
11A LEU* 3.8 8.5 - - + +
12A ILE 2.7 3.2 + - - -
13A LYS* 1.4 69.0 - - - +
15A ILE* 1.3 76.4 + - + +
16A PHE 3.2 3.6 - - - -
17A ASP* 2.6 21.9 + - - +
20A SER* 4.8 0.7 + - - -
205A THR* 5.3 11.0 + - - +
206A THR 5.8 0.2 + - - -
255A ILE* 4.0 24.5 - - + +
256A GLY 5.1 2.0 - - - +
257A LEU* 4.3 19.7 - - + -
343A LYS* 3.6 50.7 - - + +
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Residues in contact with ILE 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 LEU* 2.7 61.0 + - + +
12A ILE* 3.9 3.8 - - - +
14A MET* 1.3 83.6 - - + +
16A PHE* 1.3 66.6 + - + +
17A ASP 3.5 0.7 - - - -
21A MET* 5.5 0.7 - - - +
113A ALA* 5.2 1.4 - - - +
136A LEU* 4.4 9.9 - - + -
205A THR 3.9 13.9 - - - +
206A THR* 5.3 3.3 - - - -
208A PHE* 4.4 0.9 - - + -
209A ALA* 3.2 34.7 + - - +
212A LEU* 3.9 23.8 - - + -
257A LEU* 3.1 34.1 - - + -
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Residues in contact with PHE 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 ILE* 2.9 29.1 + - + +
13A LYS* 4.5 2.7 - - - +
15A ILE* 1.3 87.7 - - + +
17A ASP* 1.4 60.1 + - - +
18A VAL 3.8 2.1 + - - -
21A MET* 4.0 9.9 - - + +
113A ALA 3.6 19.5 - - - -
116A LEU* 3.9 28.9 - - + -
117A LEU* 3.4 37.4 - - + +
132A ASN* 3.5 45.5 + - + +
135A LYS* 4.6 1.1 - - - -
136A LEU* 3.2 33.0 - - + -
209A ALA* 4.6 7.2 - - + -
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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