Contacts of the helix formed by residues 16 - 28 (chain E) in PDB entry 5GJQ
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 16 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E THR* 4.1 7.2 - - + -
9E VAL 3.4 20.0 - - - +
10E PHE* 3.6 30.3 - - + -
15E HIS* 1.3 70.1 - - - +
17E PHE* 1.3 67.1 + - - +
18E GLN 3.3 1.6 - - - -
19E VAL* 3.1 36.2 + - + +
20E GLU* 3.2 15.5 + - - +
119E THR* 5.1 2.0 - - - -
81F LEU* 4.3 15.0 - - + -
84F ASP* 5.3 0.9 - - - +
135F ARG* 3.3 48.7 - - - +
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Residues in contact with PHE 17 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E VAL 4.4 4.2 + - - -
11E SER* 3.7 27.1 - - - +
12E PRO* 5.7 0.9 - - + -
13E ASP* 4.3 10.8 - - - -
15E HIS* 3.6 18.8 + + + -
16E LEU* 1.3 72.9 - - - +
18E GLN* 1.3 66.7 + - + +
20E GLU* 3.1 26.6 + - - +
21E TYR* 2.9 61.8 + + + -
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Residues in contact with GLN 18 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 4.0 20.3 - - - +
12D PHE* 2.7 66.8 + - - +
7E ILE* 3.6 35.6 + - + +
8E THR* 3.8 21.3 - - + +
16E LEU* 3.3 0.8 + - - +
17E PHE* 1.3 79.1 - - + +
19E VAL* 1.3 58.9 + - - +
21E TYR* 3.4 9.2 + - - -
22E ALA* 3.0 23.7 + - - +
125E ARG* 5.5 0.5 - - - +
126E PRO* 4.3 10.5 - - + -
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Residues in contact with VAL 19 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E THR* 4.5 4.3 - - + -
16E LEU* 3.1 38.0 + - + +
18E GLN* 1.3 76.7 - - - +
20E GLU* 1.3 60.4 + - + +
22E ALA* 3.4 6.8 + - - +
23E GLN* 2.9 35.7 + - - +
119E THR* 4.2 19.7 - - + -
126E PRO* 4.2 9.9 - - + -
149E PRO* 3.7 23.6 - - + +
150E SER* 3.8 22.7 - - - +
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Residues in contact with GLU 20 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15E HIS* 3.0 33.3 - - + +
16E LEU 3.2 12.1 + - - +
17E PHE* 3.1 30.8 + - - +
19E VAL* 1.3 79.0 - - + +
21E TYR* 1.3 64.4 + - + +
23E GLN* 3.1 19.8 + - - +
24E GLU* 3.0 30.2 + - - +
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Residues in contact with TYR 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.0 46.7 - - + -
13D SER 3.4 7.4 - - - +
14D PRO* 3.3 52.2 - - + +
16D GLY* 2.8 25.5 - - - -
17E PHE* 2.9 57.5 + + + +
18E GLN* 3.9 9.2 - - - +
20E GLU* 1.3 79.5 - - + +
22E ALA* 1.3 66.5 + - - +
24E GLU* 3.1 6.7 + - + -
25E ALA 3.0 4.9 + - - -
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Residues in contact with ALA 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 3.2 34.7 - - + -
18E GLN 3.0 9.8 + - - +
19E VAL* 3.4 11.9 - - - +
21E TYR* 1.3 78.7 - - - +
23E GLN* 1.3 57.2 + - - +
25E ALA* 3.1 6.1 + - - +
26E VAL* 3.0 30.4 + - - +
126E PRO* 4.4 3.1 - - + -
127E PHE 4.1 2.2 - - - +
128E GLY* 4.1 9.0 - - - -
149E PRO* 4.0 17.7 - - + -
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Residues in contact with GLN 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19E VAL* 2.9 28.1 + - - +
20E GLU* 3.1 22.1 + - - +
22E ALA* 1.3 72.0 - - - +
24E GLU* 1.3 60.7 - - - +
26E VAL* 3.3 11.6 + - + +
27E LYS* 2.9 25.8 + - - +
148E ASP* 2.9 34.4 + - - +
149E PRO* 4.0 15.9 - - + -
150E SER* 4.8 2.4 - - - -
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Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D PRO 3.5 19.3 - - - +
15D GLU* 3.0 26.4 - - - +
20E GLU 3.0 17.0 + - - +
21E TYR* 3.2 9.9 - - + +
23E GLN* 1.3 75.0 - - - +
25E ALA* 1.3 61.6 + - - +
27E LYS* 2.8 29.1 + - - +
28E LYS* 3.0 18.5 + - - +
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Residues in contact with ALA 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D PHE* 4.1 9.4 - - + -
15D GLU 4.5 0.9 - - - -
16D GLY* 2.8 30.7 - - - +
21E TYR 3.0 4.2 + - - +
22E ALA 3.3 10.3 - - - +
24E GLU* 1.3 79.5 - - - +
26E VAL* 1.3 61.4 + - - +
28E LYS* 3.3 16.8 + - - +
29E GLY* 3.7 6.1 + - - -
75E GLY* 4.0 11.9 - - - +
76E LEU* 4.2 21.8 - - + +
128E GLY 4.6 1.1 - - - +
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Residues in contact with VAL 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA 3.0 20.1 + - - +
23E GLN* 3.3 9.6 - - + +
25E ALA* 1.3 75.3 - - - +
27E LYS* 1.3 57.2 + - - +
29E GLY* 2.8 23.4 + - - -
74E ALA* 3.5 20.5 - - + +
75E GLY* 3.9 7.0 - - - -
128E GLY 3.7 1.5 + - - +
129E ILE* 3.6 26.7 - - - +
130E SER* 3.4 32.1 - - - +
149E PRO* 3.8 9.6 - - + -
161E ILE* 5.2 1.1 - - + -
162E GLY* 3.7 14.9 - - - +
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Residues in contact with LYS 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E GLN 2.9 13.2 + - - +
24E GLU* 2.8 22.4 + - - +
26E VAL* 1.3 75.8 - - - +
28E LYS* 1.3 56.4 + - + +
29E GLY 3.3 0.9 - - - -
162E GLY 4.4 9.2 - - - +
163E ARG* 3.5 23.9 - - - +
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Residues in contact with LYS 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15D GLU* 3.3 50.8 + - - +
16D GLY 5.1 2.7 - - - +
17D ARG* 4.0 19.6 - - + +
24E GLU* 3.0 14.6 + - - +
25E ALA* 3.7 12.6 - - - +
26E VAL 3.1 0.8 + - - -
27E LYS* 1.3 76.3 - - + +
29E GLY* 1.3 62.3 + - - +
163E ARG* 5.0 3.6 - - - +
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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