Contacts of the helix formed by residues 14 - 22 (chain C) in PDB entry 4GTU
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 HIS 14 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ARG* 3.1 43.2 + - + +
11C GLY 3.7 6.0 + - - +
13C ALA* 1.3 74.4 - - - +
15C ALA* 1.3 63.8 + - - +
16C ILE 3.4 0.2 - - - -
17C ARG* 3.5 16.9 + - + +
18C LEU* 3.2 47.1 + - + +
160C TYR* 4.3 10.5 - - - -
161C ASP* 3.0 28.5 - - + +
164C ASP* 5.2 0.6 + - - -
196C TYR* 5.9 1.1 - + - -
202C PHE* 3.8 27.5 - + - -
203C LEU 3.2 25.6 + - - -
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Residues in contact with ALA 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C LEU 4.6 5.8 + - - +
13C ALA 2.5 7.1 + - - +
14C HIS* 1.3 71.8 - - - +
16C ILE* 1.3 67.5 + - + +
18C LEU* 2.8 27.3 + - - +
19C LEU* 3.0 11.1 + - - +
76C LEU* 4.2 15.3 - - + -
157C PHE* 4.6 6.0 - - + +
158C LEU* 3.9 36.3 - - + +
161C ASP* 4.8 8.0 + - + +
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Residues in contact with ILE 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.7 30.3 - - + -
12C LEU 4.2 4.9 - - - +
13C ALA* 2.6 28.3 + - - +
15C ALA* 1.3 71.1 - - + +
17C ARG* 1.3 57.9 + - + +
19C LEU* 2.9 7.3 + - - +
20C LEU* 2.9 43.4 + - + +
60C PRO* 5.5 2.2 - - + -
62C LEU* 5.4 0.4 - - + -
72C SER* 3.7 17.3 - - - +
75C ILE* 3.9 29.6 - - + -
76C LEU* 3.5 33.9 - - + -
79C ILE* 4.6 4.5 - - + -
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Residues in contact with ARG 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C LEU* 3.9 23.6 - - + +
6C TYR* 4.2 4.6 - - - +
7C TRP 3.9 9.5 + - - -
9C ILE 3.4 13.9 + - - -
10C ARG* 3.4 27.7 + - - +
13C ALA* 3.1 27.5 + - - +
14C HIS* 3.5 21.0 + - - +
15C ALA 3.2 0.6 - - - -
16C ILE* 1.3 74.5 - - - +
18C LEU* 1.3 60.8 + - - +
20C LEU* 4.0 8.8 - - + +
21C GLU* 3.2 29.5 + - - +
27C TYR* 4.3 7.6 + - + +
29C GLU* 5.5 5.2 + - - +
31C LYS* 5.9 3.0 - - - +
196C TYR* 3.8 29.1 - - + +
201C ARG 5.2 1.3 - - - -
203C LEU* 3.4 31.3 + - - +
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Residues in contact with LEU 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C HIS* 3.2 46.0 + - + +
15C ALA* 2.8 13.9 + - - +
17C ARG* 1.3 71.9 - - + +
19C LEU* 1.3 69.6 + - - +
21C GLU* 4.1 1.8 - - - +
22C TYR* 3.1 21.3 + - - +
157C PHE* 3.6 30.8 - - + +
160C TYR* 4.0 23.1 - - + -
187C PHE* 4.3 15.9 - - + -
193C ILE* 4.9 12.0 - - + +
196C TYR* 4.7 19.3 - - + -
197C MET* 5.3 6.5 - - + -
202C PHE* 4.8 5.6 - - + -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ALA 3.0 8.9 + - - +
16C ILE* 2.9 10.8 + - - +
18C LEU* 1.3 76.4 - - - +
20C LEU* 1.3 51.3 + - + +
22C TYR* 2.7 25.4 + - - +
23C THR* 2.7 20.9 + - + +
76C LEU* 3.6 36.1 - - + +
79C ILE* 3.9 33.9 - - + -
80C ALA 4.7 2.0 - - - +
85C LEU* 3.8 21.3 - - + -
154C PHE* 4.2 10.5 - - + -
157C PHE* 3.7 37.1 - - + -
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C MET* 4.3 12.3 - - + -
4C LEU* 4.4 13.0 - - + -
16C ILE* 2.9 38.6 + - + +
17C ARG* 4.0 3.8 - - - +
19C LEU* 1.3 71.1 - - - +
21C GLU* 1.3 57.5 + - - +
23C THR* 3.1 6.3 + - - -
24C ASP* 2.8 26.2 + - - -
25C SER* 3.1 31.2 + - - +
27C TYR* 3.6 45.9 - - + -
62C LEU* 5.0 5.8 - - + -
79C ILE* 3.6 26.2 - - + -
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Residues in contact with GLU 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ARG 3.2 13.3 + - - +
18C LEU 4.1 2.7 - - - +
20C LEU* 1.3 77.5 - - - +
22C TYR* 1.3 61.2 + - - +
24C ASP* 3.4 16.9 + - - +
27C TYR* 2.7 38.6 + - - +
192C LYS* 4.0 15.7 - - - +
193C ILE* 6.1 0.7 - - - -
196C TYR* 3.4 35.0 + - + +
201C ARG* 3.1 35.6 + - - -
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU 3.1 14.7 + - - +
19C LEU* 2.7 15.3 + - + +
21C GLU* 1.3 72.7 - - - +
23C THR* 1.3 69.1 + - + -
24C ASP* 3.2 2.6 + - - +
85C LEU* 3.6 33.2 - - + +
152C ILE* 3.2 41.5 - - + +
157C PHE* 3.5 24.7 - + + -
190C LEU* 4.5 8.3 - - + -
192C LYS* 3.3 44.0 - - - +
193C ILE* 3.7 22.3 - - + +
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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