Contacts of the helix formed by residues 13 - 23 (chain B) in PDB entry 6JGW
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 ALA 13 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7B ALA* 4.9 1.1 - - - -
12B CYS* 1.3 77.5 - - - +
14B VAL* 1.3 66.8 + - - +
15B GLU* 4.3 10.1 - - + +
16B THR* 3.3 19.9 + - - +
17B ILE* 3.2 17.8 + - - +
17D T 4.7 9.4 - - - +
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Residues in contact with VAL 14 (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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3B ILE* 3.8 22.8 - - + +
4B GLY* 4.3 11.9 - - - +
7B ALA* 3.9 21.1 - - + +
12B CYS 3.6 0.2 + - - -
13B ALA* 1.3 73.0 - - - +
15B GLU* 1.3 64.5 + - - +
17B ILE* 3.0 11.5 + - - +
18B ARG* 2.9 63.4 + - - +
6C C 4.8 5.6 - - - +
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Residues in contact with GLU 15 (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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13B ALA* 3.4 6.8 - - + +
14B VAL* 1.3 83.9 + - - +
16B THR* 1.3 52.9 + - - +
18B ARG* 3.2 27.9 + - + +
19B TYR* 2.6 37.6 + - - +
22B ARG* 4.7 1.6 + - - +
9C A 5.6 1.6 - - - +
17D T 4.1 25.5 - - + +
18D A 3.9 28.3 - - - +
19D T 4.2 19.8 - - - +
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Residues in contact with THR 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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12B CYS* 3.7 14.5 - - - -
13B ALA* 3.3 25.7 + - - +
15B GLU* 1.3 77.4 - - - +
17B ILE* 1.3 56.5 - - - -
19B TYR* 3.1 7.1 + - - +
20B TYR* 2.7 63.1 + - + +
51B ARG* 3.9 4.3 - - - +
16D C 3.7 23.4 - - - +
17D T 3.9 16.5 + - - +
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Residues in contact with ILE 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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3B ILE* 3.9 16.2 - - + +
6B LEU* 3.9 23.8 - - + -
7B ALA* 4.0 19.5 - - + +
12B CYS* 3.9 18.6 - - - +
13B ALA 3.5 13.9 - - - +
14B VAL* 3.0 9.0 + - - +
16B THR* 1.3 74.0 - - - +
18B ARG* 1.3 68.7 + - - +
20B TYR* 3.3 8.1 + - - +
21B GLU* 3.1 20.6 + - - +
26B LEU* 3.9 15.1 - - + +
39B TYR* 3.7 22.7 - - - +
47B LEU* 3.9 19.1 - - + -
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Residues in contact with ARG 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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3B ILE* 3.9 10.0 - - - +
14B VAL* 2.9 39.4 + - - +
15B GLU* 3.5 31.4 + - + +
17B ILE* 1.3 77.7 - - - +
19B TYR* 1.3 61.3 + - - +
21B GLU* 3.2 21.5 - - - +
22B ARG* 3.3 26.7 + - - +
37B ARG* 3.9 28.4 + - - +
39B TYR* 5.7 0.2 - - - -
6C C 4.5 4.2 - - - -
7C C 2.6 49.0 + - - +
8C T 3.6 34.9 + - + +
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Residues in contact with TYR 19 (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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15B GLU 2.6 23.0 + - - +
16B THR* 3.3 5.4 - - - +
18B ARG* 1.3 71.3 - - - +
20B TYR* 1.3 85.1 + + - +
22B ARG* 2.9 46.6 + - - +
23B GLU* 3.0 39.5 + - + +
60B LEU* 3.5 19.3 - - + +
15D A 3.7 35.3 + - + -
16D C 3.9 37.2 - + - -
17D T 4.3 4.9 - - + -
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Residues in contact with TYR 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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16B THR* 2.7 37.3 + - + +
17B ILE* 3.8 6.1 - - - +
19B TYR* 1.3 88.4 - + - +
21B GLU* 1.3 61.2 + - - +
23B GLU* 3.4 5.5 + - + +
24B GLN 3.1 4.0 + - - -
25B LEU* 2.9 47.1 + - + +
26B LEU* 3.4 11.3 + - + -
47B LEU* 3.9 19.7 - - + -
50B ILE* 3.7 25.4 - - + -
51B ARG* 2.6 35.9 + - - -
54B ARG* 3.9 8.1 - - + +
60B LEU* 4.3 10.5 - - + -
16D C 2.7 31.1 + - - -
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Residues in contact with GLU 21 (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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17B ILE 3.1 11.2 + - - +
18B ARG* 3.2 12.7 - - - +
20B TYR* 1.3 76.9 - - - +
22B ARG* 1.3 63.2 + - + +
24B GLN* 3.1 14.2 + - - +
26B LEU* 4.0 19.0 - - + +
27B PRO 4.1 3.3 - - - +
28B GLU* 3.4 39.3 - - + +
29B PRO* 3.5 11.4 - - - +
31B ARG* 4.8 2.9 + - - -
37B ARG* 3.1 30.4 + - - +
39B TYR* 3.2 24.3 + - - -
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Residues in contact with ARG 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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15B GLU* 4.7 2.0 + - - +
18B ARG* 3.3 29.2 + - - +
19B TYR* 2.9 44.5 + - + +
21B GLU* 1.3 78.8 - - + +
23B GLU* 1.3 71.4 + - - +
24B GLN* 3.2 13.6 + - - +
9C A 5.7 3.0 + - - -
10C T 4.4 34.0 + - - +
17D T 4.9 8.7 + - - +
18D A 5.7 0.8 - - - +
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Residues in contact with GLU 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 TYR* 3.0 50.3 + - + +
20B TYR* 3.4 6.3 + - + +
21B GLU 3.2 0.4 - - - -
22B ARG* 1.3 89.4 - - - +
24B GLN* 1.3 72.1 + - - +
25B LEU* 3.2 7.8 + - + +
60B LEU* 4.6 7.9 - - + +
64B ARG* 2.8 40.2 + - - +
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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