Contacts of the helix formed by residues 11 - 22 (chain G) 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 GLY 11 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G TYR* 3.4 15.5 - - - -
9G ILE* 3.5 4.8 - - - +
10G ARG* 1.3 101.2 + - - +
12G LEU* 1.3 59.1 + - - -
13G ALA 3.0 2.6 + - - -
14G HIS* 3.6 3.6 + - - +
161G ASP* 4.8 2.4 - - - +
207G LEU 3.3 15.6 + - - -
208G TYR* 5.6 0.9 - - - -
209G THR* 6.3 0.4 - - - -
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G TYR* 3.4 21.9 + - + +
11G GLY* 1.3 71.6 - - - -
13G ALA* 1.3 56.9 + - - +
14G HIS 3.5 1.3 - - - -
15G ALA* 5.0 3.8 + - - +
16G ILE* 4.2 8.5 - - - +
59G LEU 4.3 3.4 - - - +
60G PRO* 3.4 33.1 - - + +
72G SER* 3.9 31.7 - - - +
104G MET* 4.9 19.9 - - + +
108G ASN* 5.9 4.5 - - - +
161G ASP* 5.3 4.7 - - - -
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Residues in contact with ALA 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 4.9 7.6 - - + -
6G TYR* 3.6 22.7 - - + -
10G ARG 3.3 4.5 - - - +
11G GLY 3.0 1.6 + - - -
12G LEU* 1.3 77.9 - - - +
14G HIS* 1.3 65.2 + - - +
15G ALA 3.4 2.5 - - - -
16G ILE* 3.1 21.0 + - - +
17G ARG* 3.1 45.5 + - - +
60G PRO* 4.9 6.3 - - + -
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Residues in contact with HIS 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ARG* 3.4 47.8 + - + +
11G GLY 3.6 3.7 + - - +
12G LEU 3.5 0.4 - - - -
13G ALA* 1.3 75.5 - - - +
15G ALA* 1.3 63.5 + - - +
17G ARG* 3.2 26.0 + - - +
18G LEU* 3.2 38.0 + - + +
160G TYR* 4.7 7.5 - + - -
161G ASP* 3.3 30.1 - - + +
164G ASP* 4.4 6.6 + - - -
202G PHE* 3.8 31.6 - + - -
203G LEU 3.6 14.2 + - - -
204G PRO* 4.4 1.6 - - + -
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Residues in contact with ALA 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU 5.0 3.2 + - - +
13G ALA 3.4 0.6 - - - -
14G HIS* 1.3 78.8 - - - +
16G ILE* 1.3 64.6 + - + +
18G LEU* 3.1 15.4 + - - +
19G LEU* 3.0 23.2 + - - +
76G LEU* 4.4 19.7 - - + -
157G PHE* 4.3 9.0 - - + +
158G LEU* 4.3 27.6 - - + +
161G ASP* 4.4 10.7 + - + +
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 3.2 34.5 - - + -
12G LEU 4.2 16.2 - - - +
13G ALA* 3.1 11.3 + - - +
15G ALA* 1.3 80.0 - - + +
17G ARG* 1.3 59.5 + - + +
19G LEU* 3.4 2.5 + - - +
20G LEU* 2.9 46.3 + - + +
60G PRO* 5.2 3.1 - - + -
62G LEU* 6.4 0.2 - - + -
72G SER* 3.9 19.5 - - - +
75G ILE* 4.1 24.2 - - + -
76G LEU* 3.5 35.2 - - + -
79G ILE* 4.8 3.5 - - + +
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Residues in contact with ARG 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4G LEU* 5.2 8.1 - - + +
6G TYR* 4.0 10.9 - - - +
7G TRP 4.2 4.9 + - - -
8G ASP 5.8 0.2 + - - -
9G ILE 3.8 15.5 + - - -
10G ARG* 3.4 15.2 + - - +
13G ALA* 3.1 48.9 + - - +
14G HIS* 3.2 17.1 + - - +
16G ILE* 1.3 82.6 - - + +
18G LEU* 1.3 62.2 + - + +
20G LEU* 4.3 5.1 - - - +
21G GLU* 3.3 31.3 + - + +
27G TYR* 5.4 9.4 - - + +
29G GLU* 3.8 25.9 + - - +
31G LYS* 5.2 5.1 - - - +
196G TYR* 3.8 29.3 - - + +
201G ARG 5.1 1.8 - - - -
203G LEU* 4.8 18.4 + - - +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G HIS* 3.2 34.5 + - + +
15G ALA* 3.1 9.3 + - - +
17G ARG* 1.3 77.3 - - + +
19G LEU* 1.3 66.4 + - - +
21G GLU* 4.0 1.8 - - - +
22G TYR* 3.0 25.8 + - - +
157G PHE* 3.6 23.6 - - + +
160G TYR* 3.7 17.0 - - + -
187G PHE* 3.7 29.4 - - + -
193G ILE* 4.1 8.9 - - + +
196G TYR* 4.4 22.4 - - + -
197G MET* 4.7 11.2 - - + -
202G PHE* 4.6 9.0 - - + -
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G ALA 3.0 14.2 + - - +
16G ILE 3.7 3.1 - - - +
18G LEU* 1.3 80.6 - - - +
20G LEU* 1.3 65.4 + - - +
22G TYR* 3.2 1.9 + - - +
23G THR* 3.1 31.3 + - + +
76G LEU* 3.6 43.7 - - + +
79G ILE* 4.0 25.8 - - + -
80G ALA* 4.7 2.2 - - - +
83G HIS* 5.8 0.2 - - + -
85G LEU* 4.2 15.5 - - + -
154G PHE* 4.2 15.5 - - + -
157G PHE* 3.5 38.1 - - + -
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Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2G MET* 3.6 31.2 - - + -
4G LEU* 3.8 22.9 - - + -
16G ILE* 2.9 40.2 + - + +
17G ARG* 4.3 4.9 - - - +
19G LEU* 1.3 79.0 - - - +
21G GLU* 1.3 62.0 + - - +
23G THR* 3.3 7.6 + - - -
25G SER* 3.1 34.1 + - - +
27G TYR* 3.9 24.9 - - + -
62G LEU* 5.2 6.5 - - + -
75G ILE* 6.4 0.2 - - + -
79G ILE* 3.9 26.2 - - + -
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Residues in contact with GLU 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG 3.3 20.0 + - - +
18G LEU 4.0 1.6 - - - +
20G LEU* 1.3 76.2 - - - +
22G TYR* 1.3 65.9 + - - +
24G ASP* 3.0 23.0 + - - +
25G SER 5.4 0.9 - - - +
27G TYR* 3.1 38.0 + - + +
192G LYS* 4.7 5.6 - - - +
193G ILE* 6.2 0.9 - - + -
196G TYR* 3.3 34.5 - - + -
201G ARG* 3.1 29.4 + - - -
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Residues in contact with TYR 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191F GLU* 4.4 11.4 + - - -
18G LEU 3.0 18.2 + - - +
19G LEU 3.2 2.9 + - - +
21G GLU* 1.3 75.6 - - - +
23G THR* 1.3 68.5 + - + +
24G ASP 3.1 2.1 + - - -
85G LEU* 5.0 7.0 - - + -
152G ILE* 4.4 21.4 - - + +
157G PHE* 3.6 23.1 - + + -
190G LEU* 3.6 28.6 - - + +
192G LYS* 3.0 64.9 + - + +
193G ILE* 3.6 23.2 - - + +
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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