Contacts of the helix formed by residues 6 - 21 (chain B) in PDB entry 2YGG
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 THR 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LEU* 1.3 78.5 - - - +
7B GLU* 1.3 68.7 + - - +
8B GLU* 3.7 6.1 + - - +
9B GLN* 3.0 36.3 + - - +
10B ILE* 2.9 30.4 + - - +
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Residues in contact with GLU 7 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B LEU 5.0 1.7 - - - +
6B THR* 1.3 78.3 - - - +
8B GLU* 1.3 62.3 + - + +
10B ILE* 3.5 14.2 + - - +
11B ALA* 3.1 25.8 + - - +
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Residues in contact with GLU 8 (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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670A ARG* 4.3 9.0 + - - +
6B THR* 3.4 5.9 + - - +
7B GLU* 1.3 77.9 - - + +
9B GLN* 1.3 60.1 + - + +
11B ALA* 3.3 8.9 + - - +
12B GLU* 3.0 36.9 + - - +
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Residues in contact with GLN 9 (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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5B LEU* 3.1 19.9 - - + +
6B THR* 3.0 44.7 + - - +
8B GLU* 1.3 79.4 - - + +
10B ILE* 1.3 60.2 + - - +
12B GLU* 3.3 16.4 + - - +
13B PHE* 3.1 34.6 + - + -
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Residues in contact with ILE 10 (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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5B LEU* 4.1 19.5 - - + +
6B THR 2.9 20.5 + - - +
7B GLU* 4.0 14.6 - - - +
9B GLN* 1.3 73.8 - - - +
11B ALA* 1.3 60.0 + - - +
13B PHE* 3.2 10.8 + - + +
14B LYS* 2.9 52.5 + - + +
66B PHE* 4.8 11.0 - - + -
70B LEU* 5.7 9.0 - - + -
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Residues in contact with ALA 11 (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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670A ARG* 3.4 21.1 + - - +
7B GLU 3.1 15.5 + - - +
8B GLU* 3.3 13.9 - - - +
10B ILE* 1.3 77.1 - - - +
12B GLU* 1.3 61.6 + - - +
14B LYS* 3.3 12.2 + - - +
15B GLU* 3.0 24.9 + - - +
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Residues in contact with GLU 12 (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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663A TRP* 4.0 21.9 - - + -
666A MET* 3.7 25.8 - - + +
667A LEU* 4.3 15.8 - - - +
670A ARG* 3.8 29.5 + - - +
8B GLU* 3.0 22.6 + - - +
9B GLN* 3.6 18.4 - - - +
10B ILE 3.3 0.2 - - - -
11B ALA* 1.3 75.5 - - - +
13B PHE* 1.3 57.3 + - - +
15B GLU 3.4 0.2 + - - -
16B ALA* 2.9 29.5 + - - +
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Residues in contact with PHE 13 (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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663A TRP* 3.3 33.0 - + - -
5B LEU* 5.2 7.6 - - + -
9B GLN* 3.1 32.4 + - + -
10B ILE* 3.2 10.2 + - + +
12B GLU* 1.3 75.3 - - - +
14B LYS* 1.3 55.6 + - - +
16B ALA* 3.3 1.4 + - - -
17B PHE* 2.7 36.7 + - - +
66B PHE* 3.5 20.4 - - + -
69B PHE* 3.4 10.6 - + - -
70B LEU* 3.5 25.1 - - + -
73B MET* 3.5 29.8 - - + -
74B ALA* 5.0 6.5 - - + -
77B MET* 4.0 19.5 - - - -
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Residues in contact with LYS 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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10B ILE* 2.9 35.7 + - + +
11B ALA* 3.5 13.4 - - - +
13B PHE* 1.3 71.9 - - - +
15B GLU* 1.3 52.9 + - - +
17B PHE* 3.3 5.1 + - - +
18B SER* 2.7 35.3 + - - -
66B PHE* 3.5 22.6 - - + -
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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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666A MET* 3.4 18.5 - - + +
669A ARG* 2.6 56.1 + - - +
670A ARG* 3.1 17.8 + - - +
11B ALA 3.0 16.3 + - - +
12B GLU 3.8 3.4 - - - +
14B LYS* 1.3 72.1 - - - +
16B ALA* 1.3 68.3 + - - +
18B SER* 2.6 24.4 + - - +
19B LEU* 3.0 25.7 + - + +
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Residues in contact with ALA 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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662A ALA* 4.3 4.0 - - + +
663A TRP* 3.9 33.4 - - + +
666A MET* 4.1 6.6 - - + +
12B GLU 2.9 18.1 + - - +
13B PHE 3.5 4.7 - - - +
15B GLU* 1.3 77.8 - - - +
17B PHE* 1.3 63.4 + - - +
19B LEU* 3.2 23.6 + - - +
20B PHE* 3.4 11.6 - - - -
69B PHE* 3.8 15.9 - - + -
73B MET* 4.6 1.3 - - + -
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Residues in contact with PHE 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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13B PHE 2.7 22.2 + - - +
14B LYS* 3.4 5.6 - - - +
16B ALA* 1.3 73.3 - - - +
18B SER* 1.3 57.8 + - - +
20B PHE* 3.0 11.2 + - + +
21B ASP* 3.0 36.1 + - + +
26B GLY* 3.6 36.6 - - - -
27B THR* 3.9 1.3 - - - -
28B ILE* 3.2 32.8 - - + -
64B ILE 3.8 8.3 - - - -
66B PHE* 3.3 39.3 - + + -
69B PHE* 3.6 35.1 - + + -
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Residues in contact with SER 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 LYS 2.7 16.7 + - - -
15B GLU* 2.6 31.9 + - - +
17B PHE* 1.3 69.3 - - - +
19B LEU* 1.3 66.6 + - - +
20B PHE 2.9 3.1 + - - -
21B ASP* 3.1 28.4 + - - +
22B LYS* 3.9 7.3 + - - +
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Residues in contact with LEU 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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662A ALA* 4.3 26.0 - - + +
665A GLN* 3.2 36.1 - - + +
666A MET* 4.8 4.5 - - + +
15B GLU* 3.0 41.8 + - + +
16B ALA* 3.2 15.9 + - - +
18B SER* 1.3 77.1 + - - +
20B PHE* 1.3 56.9 + - + +
22B LYS* 2.9 29.2 - - - +
36B VAL* 3.7 11.0 - - + +
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Residues in contact with PHE 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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658A PRO* 3.3 25.1 - - + -
659A TYR* 3.7 26.0 - + - -
662A ALA* 3.4 23.8 - - + -
16B ALA 3.4 15.3 - - - -
17B PHE* 3.0 7.5 + - - +
18B SER 2.9 0.4 - - - -
19B LEU* 1.3 82.6 - - + +
21B ASP* 1.3 57.3 + - - +
22B LYS* 3.3 11.1 + - - +
28B ILE* 3.4 36.3 - - + -
32B GLU* 3.5 27.0 - - + +
33B LEU* 4.0 18.8 - - + -
36B VAL* 3.8 33.6 - - + +
69B PHE* 4.4 13.5 - + - -
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Residues in contact with ASP 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 PHE* 3.0 31.1 + - + +
18B SER* 3.1 15.3 + - - +
20B PHE* 1.3 71.8 - - - +
22B LYS* 1.3 62.6 + - - +
23B ASP* 2.9 9.6 - - - +
24B GLY* 3.3 19.7 + - - -
25B ASP* 3.0 1.2 - - - +
26B GLY* 2.9 26.2 + - - -
27B THR 2.8 15.7 - - - +
28B ILE* 4.9 1.1 - - + -
32B GLU* 3.9 4.0 - - - -
1153B CA 2.6 28.2 - - - -
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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