Contacts of the helix formed by residues 15 - 26 (chain B) in PDB entry 3GTU
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 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B TYR* 4.0 7.6 - - - -
13B ILE* 3.6 6.3 - - - +
14B ARG* 1.3 85.9 - - - +
16B LEU* 1.3 60.7 + - - -
18B HIS* 3.5 12.1 + - - +
111B ARG* 6.2 0.4 - - - -
165B ASP* 4.3 11.1 - - - +
169B GLN* 5.0 7.2 - - - +
211B ILE 3.0 16.7 + - - -
212B ASN* 5.1 3.4 - - - -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B TYR* 3.1 24.3 + - + +
15B GLY* 1.3 71.5 - - - -
17B ALA* 1.3 61.7 - - - +
18B HIS 3.2 1.1 + - - -
19B ALA* 4.1 9.1 + - - +
20B ILE* 4.1 12.3 - - - +
63B LEU 4.6 4.9 - - - +
64B PRO* 4.3 12.6 - - + -
76B SER* 3.5 32.0 + - - +
80B LEU* 5.9 0.7 - - - +
108B MET* 5.9 3.4 - - + -
111B ARG* 3.8 42.7 + - - +
115B ILE* 5.3 7.6 - - + -
165B ASP* 5.7 1.1 - - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.7 9.6 - - + -
10B TYR* 3.4 35.7 - - + -
14B ARG 3.2 2.0 + - - -
16B LEU* 1.3 77.6 - - - +
18B HIS* 1.3 58.3 + - - +
19B ALA 3.4 0.4 - - - -
20B ILE* 3.0 12.4 + - + +
21B ARG* 2.8 51.3 + - + +
64B PRO* 4.8 4.9 - - + -
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Residues in contact with HIS 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ARG* 3.1 51.2 + - + +
15B GLY 3.6 9.0 - - - +
16B LEU 3.2 0.6 - - - -
17B ALA* 1.3 75.8 - - - +
19B ALA* 1.3 61.8 + - - +
21B ARG* 3.5 9.2 + - - +
22B LEU* 3.1 60.5 + - + +
164B TYR* 4.1 9.3 + - - -
165B ASP* 3.2 27.6 - - + +
168B ASP* 4.6 0.4 + - - -
200B TYR* 4.6 6.5 + + - -
201B LEU* 4.8 0.7 - - + -
206B PHE* 3.2 37.6 - + - -
209B MET* 5.8 0.6 - - - +
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Residues in contact with ALA 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU 4.1 6.3 + - - +
17B ALA 3.4 0.4 - - - -
18B HIS* 1.3 79.5 - - - +
20B ILE* 1.3 57.2 + - - +
22B LEU* 3.6 8.1 + - - +
23B LEU* 3.0 28.8 + - - +
80B LEU* 3.8 18.3 - - + +
111B ARG* 5.4 0.9 - - - +
161B PHE* 3.9 32.4 - - - +
162B LEU* 4.3 15.9 - - + +
165B ASP* 4.6 8.8 - - + +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.9 17.9 - - + -
16B LEU 4.1 13.0 - - - +
17B ALA* 3.0 11.8 + - - +
19B ALA* 1.3 73.9 - - - +
21B ARG* 1.3 59.7 + - - +
23B LEU* 3.3 2.2 + - - +
24B LEU* 2.9 34.4 + - + +
64B PRO* 3.9 30.3 - - + -
76B SER* 4.4 8.3 - - - +
79B ILE* 3.7 37.0 - - + -
80B LEU* 3.9 25.6 - - + -
83B ILE* 4.1 13.0 - - + -
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Residues in contact with ARG 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B LEU* 4.0 9.3 - - + +
10B TYR* 4.1 3.6 - - - +
11B TRP 3.5 10.1 + - - -
13B ILE 3.0 29.1 + - - -
14B ARG* 3.2 24.0 + - - +
17B ALA* 2.8 35.2 + - - +
18B HIS* 3.8 10.6 + - - +
20B ILE* 1.3 70.8 - - - +
22B LEU* 1.3 58.9 + - - +
24B LEU* 3.4 7.8 + - - +
25B GLU* 3.0 35.5 + - - +
31B TYR* 4.2 8.9 + - - +
33B GLU* 3.1 34.3 + - - +
35B ARG* 3.2 19.9 - - - +
200B TYR* 3.4 29.6 - - + +
209B MET* 3.6 14.3 - - - +
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Residues in contact with LEU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B HIS* 3.1 46.3 + - + +
19B ALA* 3.8 7.9 - - - +
21B ARG* 1.3 76.2 - - - +
23B LEU* 1.3 59.7 + - - +
25B GLU* 3.3 5.8 + - + +
26B PHE* 2.8 31.5 + - - +
161B PHE* 4.0 14.6 - - + +
164B TYR* 3.9 23.1 - - + -
191B PHE* 4.3 6.3 - - + -
197B ILE* 3.8 29.2 - - + +
200B TYR* 3.6 32.5 - - + -
201B LEU* 4.4 6.3 - - + -
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Residues in contact with LEU 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B ALA 3.0 17.8 + - - +
20B ILE* 3.3 5.8 + - - +
22B LEU* 1.3 76.6 - - - +
24B LEU* 1.3 55.8 + - - +
26B PHE* 3.7 0.3 - - - +
27B THR* 2.8 49.7 + - + +
80B LEU* 3.7 40.8 - - + +
83B ILE* 4.1 16.8 - - + -
84B ALA* 4.0 18.6 - - + +
89B MET* 4.0 8.5 - - - -
158B PHE* 4.4 5.8 - - + -
161B PHE* 3.7 34.0 - - + -
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Residues in contact with LEU 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B MET* 4.0 10.5 - - - -
8B LEU* 4.0 19.3 - - + -
20B ILE* 2.9 27.1 + - + +
21B ARG* 3.6 4.5 - - - +
22B LEU 3.3 0.2 - - - -
23B LEU* 1.3 76.3 - - - +
25B GLU* 1.3 59.5 + - - +
27B THR* 3.3 4.9 + - - -
28B ASP 3.3 2.9 + - - -
29B THR* 2.9 59.8 + - + +
31B TYR* 3.7 46.4 - - + -
66B LEU* 5.2 2.5 - - + -
83B ILE* 3.6 25.4 - - + -
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Residues in contact with GLU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ARG 3.0 20.2 + - - +
22B LEU* 3.5 9.6 - - - +
24B LEU* 1.3 74.8 - - - +
26B PHE* 1.3 65.4 + - - +
28B ASP* 2.9 18.6 + - - +
29B THR 5.6 0.2 - - - -
31B TYR* 3.2 26.9 + - - +
196B LYS* 3.9 23.3 - - + +
197B ILE* 5.5 0.7 - - + -
200B TYR* 3.7 36.6 - - + +
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Residues in contact with PHE 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LEU 2.8 20.0 + - - +
23B LEU 3.7 3.1 - - - +
25B GLU* 1.3 74.4 - - - +
27B THR* 1.3 70.1 + - + +
28B ASP* 3.2 5.4 + - - +
89B MET* 3.5 25.8 - - + -
156B LEU* 3.6 16.4 - - + -
161B PHE* 3.7 23.1 - + + -
194B LEU* 4.0 36.8 - - + -
196B LYS* 3.5 39.1 - - + +
197B ILE* 4.0 8.3 - - + +
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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