Contacts of the helix formed by residues 10 - 18 (chain A) in PDB entry 5H4G
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 ASP 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PHE* 1.3 75.6 - - - +
11A SER* 1.3 60.0 + - - +
12A LEU* 3.7 7.7 + - - +
13A ALA* 3.0 25.5 + - - +
14A LEU* 2.8 26.7 + - - +
41A THR* 3.6 3.6 - - - -
97A GLU* 5.4 1.8 - - - +
101A THR* 4.1 14.6 - - + +
112A LEU* 3.7 3.9 - - + +
113A VAL 3.5 4.9 + - - -
114A THR* 2.7 28.4 + - - -
115A ASP 4.8 1.0 + - - -
119A ARG* 3.7 11.2 + - - +
120A TYR* 2.7 28.3 + - - +
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Residues in contact with SER 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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10A ASP* 1.3 75.2 - - - +
12A LEU* 1.3 66.5 + - - +
14A LEU* 3.2 3.5 + - - +
15A ILE* 2.9 38.0 + - - +
41A THR* 3.5 21.0 + - - +
44A ARG* 3.4 25.2 - - - +
45A TYR* 4.1 4.7 - - - +
97A GLU* 2.6 33.4 + - - -
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Residues in contact with LEU 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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10A ASP* 3.4 7.7 + - - +
11A SER* 1.3 82.4 + - - +
13A ALA* 1.4 61.7 + - - +
15A ILE* 3.5 18.9 + - + +
16A LYS* 3.3 19.8 + - - +
115A ASP* 4.8 10.7 - - + +
119A ARG* 5.1 17.7 - - - +
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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 PHE* 4.0 11.2 - - + -
10A ASP* 3.0 21.7 + - - +
12A LEU* 1.4 76.1 - - - +
14A LEU* 1.3 58.7 + - - +
16A LYS* 3.3 4.2 + - - +
17A MET* 3.0 32.0 + - - +
113A VAL 3.6 20.0 - - - +
114A THR* 4.2 6.3 - - - -
115A ASP* 4.2 3.7 + - - +
133A LEU* 4.1 23.7 - - + +
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Residues in contact with LEU 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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9A PHE* 4.0 27.8 - - + +
10A ASP 2.8 17.7 + - - +
11A SER* 3.2 6.7 + - - +
13A ALA* 1.3 76.0 - - - +
15A ILE* 1.3 59.1 + - - +
17A MET* 4.3 5.2 - - + +
18A HIS* 2.9 33.7 + - + +
37A LEU* 3.9 24.0 - - + -
41A THR* 4.4 9.4 - - + +
42A VAL* 5.1 3.1 - - + -
45A TYR* 3.7 37.2 - - + -
63A LEU* 5.5 2.0 - - + -
67A TYR* 3.8 30.7 - - + +
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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 SER* 2.9 27.8 + - - +
12A LEU* 3.6 21.5 - - + +
13A ALA 3.3 0.2 - - - -
14A LEU* 1.3 75.1 - - - +
16A LYS* 1.3 63.1 + - - +
18A HIS 4.1 1.0 - - - -
19A SER* 3.8 18.5 + - - -
44A ARG 4.5 9.0 - - - +
45A TYR* 3.7 23.1 - - + -
48A ALA* 3.5 32.5 - - + -
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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 LEU 3.3 9.4 + - - +
13A ALA 3.3 9.8 + - - +
14A LEU 3.2 0.2 - - - -
15A ILE* 1.3 80.1 - - - +
17A MET* 1.3 57.5 + - + +
19A SER* 2.8 26.9 + - - -
22A MET* 3.0 23.1 - - + +
115A ASP* 5.1 1.6 - - - +
133A LEU* 4.3 19.5 - - + -
137A ILE* 4.7 11.0 - - + -
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Residues in contact with MET 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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9A PHE* 3.8 34.3 - - + -
13A ALA 3.0 20.2 + - - +
14A LEU* 3.9 10.1 - - + +
16A LYS* 1.3 75.8 - - + +
18A HIS* 1.3 57.6 + - + +
19A SER 3.3 4.5 + - - +
22A MET* 3.4 19.0 - - - +
25A ILE* 4.0 22.4 - - + -
26A LEU* 3.6 40.8 - - + +
29A THR* 3.5 24.7 - - - +
133A LEU* 4.1 20.0 - - + -
136A PHE* 4.2 4.0 - - + -
137A ILE* 4.4 10.8 - - - -
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Residues in contact with HIS 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 LEU* 2.9 20.5 + - + +
15A ILE 4.1 3.8 - - - -
17A MET* 1.3 76.2 - - - +
19A SER* 1.3 60.5 + - - +
20A GLN 4.1 0.2 + - - -
26A LEU* 3.5 17.4 - - + +
45A TYR* 3.0 33.1 + + + +
59A GLU* 3.6 9.1 + - - -
62A ILE* 4.3 9.4 - - + +
63A LEU* 3.5 18.2 - - + +
66A ILE* 3.4 32.8 - - + -
67A TYR* 2.9 23.5 + - - +
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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