Contacts of the helix formed by residues 12 - 22 (chain H) 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 LEU 12 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6H TYR* 3.2 18.0 + - + +
11H GLY* 1.3 71.2 - - - -
13H ALA* 1.3 62.8 + - - +
14H HIS 3.2 2.0 + - - -
15H ALA* 3.7 13.9 + - - +
16H ILE* 4.1 7.8 - - - +
59H LEU 4.7 5.6 - - - +
60H PRO* 4.4 10.3 - - + -
72H SER* 3.6 31.4 + - - +
104H MET* 5.9 7.2 - - - -
107H SER* 6.1 4.9 - - - -
108H ASN* 6.5 1.3 - - + -
161H ASP* 5.2 3.5 - - - +
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Residues in contact with ALA 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.8 3.8 - - + -
6H TYR* 3.6 23.3 - - + -
10H ARG 4.2 0.2 - - - +
11H GLY 3.3 1.4 - - - -
12H LEU* 1.3 77.8 - - - +
14H HIS* 1.3 62.2 + - - +
15H ALA 3.3 0.7 - - - -
16H ILE* 3.0 17.1 + - + +
17H ARG* 3.0 58.7 + - + +
60H PRO* 4.3 7.6 - - + -
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Residues in contact with HIS 14 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H ARG* 3.2 48.5 + - + +
11H GLY 3.7 7.4 - - - +
12H LEU 3.2 1.0 - - - -
13H ALA* 1.3 76.8 - - - +
15H ALA* 1.3 62.6 + - - +
17H ARG* 3.8 10.7 - - - +
18H LEU* 3.2 37.1 + - + +
160H TYR* 5.3 4.1 - + - -
161H ASP* 3.3 25.1 - - + +
164H ASP* 4.4 6.0 + - - -
196H TYR* 5.1 12.9 + + - -
202H PHE* 4.6 18.1 - + - -
203H LEU 3.2 27.4 + - - -
204H PRO* 4.7 1.1 - - + -
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Residues in contact with ALA 15 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H LEU 3.7 10.6 + - - +
13H ALA 3.3 0.6 - - - -
14H HIS* 1.3 79.7 - - - +
16H ILE* 1.3 62.4 + - + +
18H LEU* 3.7 5.7 + - - +
19H LEU* 3.3 15.9 + - - +
76H LEU* 3.5 30.8 - - + +
157H PHE* 4.3 9.1 - - - +
158H LEU* 4.3 23.1 - - + +
161H ASP* 4.4 19.9 + - + +
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Residues in contact with ILE 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.7 22.4 - - + -
12H LEU 4.1 5.6 - - - +
13H ALA* 3.1 19.7 - - - +
15H ALA* 1.3 76.7 - - + +
17H ARG* 1.3 65.5 + - - +
19H LEU* 3.0 14.4 + - - +
20H LEU* 3.0 23.7 + - + +
60H PRO* 3.6 35.0 - - + -
72H SER* 4.4 8.3 - - - +
75H ILE* 3.4 37.2 - - + -
76H LEU* 3.9 21.8 - - + -
79H ILE* 4.2 3.8 - - + -
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Residues in contact with ARG 17 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 3.3 21.4 - - + +
6H TYR* 3.1 37.8 - - - +
7H TRP 3.6 6.9 + - - -
9H ILE 3.1 8.7 + - - -
10H ARG* 3.5 8.5 + - - +
13H ALA* 3.1 32.2 - - - +
14H HIS* 3.8 10.5 - - - +
16H ILE* 1.3 74.0 - - - +
18H LEU* 1.3 63.4 + - - +
20H LEU* 3.2 13.1 + - - +
21H GLU* 3.0 24.8 + - - +
27H TYR* 5.3 8.4 + - + +
29H GLU* 4.9 12.6 + - - +
31H LYS* 4.2 13.4 - - - +
196H TYR* 3.9 23.3 - - + +
203H LEU* 3.1 36.4 + - - +
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Residues in contact with LEU 18 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H HIS* 3.2 28.2 + - + +
15H ALA* 3.9 5.8 - - - +
16H ILE 3.2 0.2 - - - -
17H ARG* 1.3 77.9 - - - +
19H LEU* 1.3 64.5 + - - +
21H GLU* 3.7 2.1 + - + +
22H TYR* 3.3 15.4 + - - +
157H PHE* 3.5 23.2 - - + +
160H TYR* 4.2 17.9 - - + -
187H PHE* 3.3 33.2 - - + -
193H ILE* 3.7 26.4 - - + +
196H TYR* 3.7 31.6 - - + -
197H MET* 6.1 0.4 - - + -
202H PHE* 5.8 2.2 - - + -
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H ALA 3.3 9.6 + - - +
16H ILE 3.0 8.8 + - - +
18H LEU* 1.3 77.9 - - - +
20H LEU* 1.3 58.4 + - - +
22H TYR* 3.0 5.9 + - - +
23H THR* 2.9 30.7 + - + +
76H LEU* 3.5 45.8 - - + +
79H ILE* 3.7 25.6 - - + -
80H ALA* 4.3 2.9 - - + +
85H LEU* 4.1 21.3 - - + -
154H PHE* 4.3 11.7 - - + -
157H PHE* 3.6 37.2 - - + -
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Residues in contact with LEU 20 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H MET* 4.2 11.4 - - - -
4H LEU* 3.9 30.3 - - + -
16H ILE* 3.0 20.6 + - + +
17H ARG* 3.4 7.4 - - - +
19H LEU* 1.3 79.8 - - - +
21H GLU* 1.3 62.2 + - - +
23H THR* 3.4 5.2 + - - -
24H ASP 3.1 19.8 + - - -
25H SER* 3.4 32.7 + - - +
27H TYR* 4.0 33.9 - - + -
62H LEU* 4.7 3.1 - - + -
79H ILE* 3.3 31.6 - - + -
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Residues in contact with GLU 21 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ARG 3.0 15.2 + - - +
18H LEU* 4.1 3.8 - - + +
20H LEU* 1.3 76.2 - - - +
22H TYR* 1.3 61.6 + - - +
24H ASP* 3.5 13.0 + - - +
25H SER 5.5 0.2 - - - +
27H TYR* 2.8 36.7 + - - -
192H LYS* 4.3 15.5 - - - +
193H ILE* 5.5 1.6 - - + -
196H TYR* 3.1 52.0 - - + -
201H ARG* 3.5 24.1 + - - -
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Residues in contact with TYR 22 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18H LEU 3.3 11.4 + - - +
19H LEU 3.0 8.2 + - - +
21H GLU* 1.3 76.2 - - - +
23H THR* 1.3 70.4 + - + +
24H ASP* 3.1 9.1 + - - +
85H LEU* 4.4 19.4 - - + +
152H ILE* 3.9 27.3 - - + +
157H PHE* 3.8 22.0 - + + -
190H LEU* 4.0 26.6 - - + +
192H LYS* 3.4 44.4 - - + +
193H ILE* 3.4 26.0 - - + +
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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