Contacts of the helix formed by residues 6 - 19 (chain Q) in PDB entry 2J28
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 6 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29B U 4.2 18.8 - - - -
583B G 3.3 18.8 + - - -
4Q LYS 2.7 9.3 + - - -
5Q ARG* 1.3 74.8 - - - +
7Q VAL* 1.3 62.7 + - - +
8Q ILE* 3.1 5.3 - - - +
9Q ALA* 3.7 2.8 - - - +
10Q ARG* 3.0 32.4 + - - +
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Residues in contact with VAL 7 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B U 4.2 18.8 + - - +
30B G 5.1 8.7 - - - +
1198B U 5.8 1.6 - - - +
1215B G 3.4 29.8 - - - +
1216B G 3.3 34.0 + - - +
4Q LYS 5.7 0.4 - - - +
6Q GLY* 1.3 75.4 - - - +
8Q ILE* 1.3 81.7 + - + +
10Q ARG* 4.3 1.3 - - - +
11Q ALA* 3.3 23.3 + - + +
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Residues in contact with ILE 8 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197B G 4.1 9.6 - - - +
1198B U 3.4 49.1 - - - +
1227B G 5.3 8.1 - - - +
1250B G 5.1 10.5 - - - +
1251B C 4.6 7.4 - - - +
3Q VAL 5.5 1.3 - - - +
5Q ARG* 5.0 10.1 - - + -
6Q GLY 4.7 6.3 - - - +
7Q VAL* 1.3 96.5 - - + +
9Q ALA* 1.3 57.3 + - - +
11Q ALA* 3.2 6.9 + - - +
12Q ARG* 2.8 37.4 + - + +
15Q LYS* 5.2 0.3 + - - -
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Residues in contact with ALA 9 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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583B G 3.8 22.0 - - - +
1251B C 3.6 24.4 + - - +
5Q ARG* 4.1 9.4 - - + +
6Q GLY* 3.4 16.6 + - - +
8Q ILE* 1.3 79.0 - - - +
10Q ARG* 1.3 64.8 + - - +
12Q ARG* 2.8 23.9 + - - +
13Q HIS* 3.4 4.0 + - - +
31Q TYR* 4.7 10.6 + - - +
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Residues in contact with ARG 10 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B A 3.5 20.8 + - - -
29B U 3.5 26.3 + - - -
513B A 3.1 58.1 + - - -
514B A 5.0 5.4 - - - -
582B A 4.4 23.4 + - - +
583B G 4.5 3.4 + - - +
1216B G 3.8 30.5 + - - +
1217B U 3.9 11.4 - - - +
6Q GLY 3.0 15.9 + - - +
7Q VAL 4.3 2.9 - - - +
9Q ALA* 1.3 76.9 - - - +
11Q ALA* 1.3 64.3 + - - +
13Q HIS* 3.7 1.4 + - - +
14Q LYS* 3.0 34.5 + - + +
31Q TYR* 5.8 2.4 - - - -
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Residues in contact with ALA 11 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q VAL* 3.3 15.1 + - + +
8Q ILE* 3.2 11.4 + - - +
9Q ALA 3.1 0.2 - - - -
10Q ARG* 1.3 77.5 - - - +
12Q ARG* 1.3 68.1 + - - +
14Q LYS* 2.9 26.7 + - - +
15Q LYS* 3.2 21.3 + - - +
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Residues in contact with ARG 12 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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812B C 2.8 41.6 + - - -
813B U 5.5 2.4 + - - -
1226B A 5.7 0.7 - - - -
1227B G 4.5 15.0 - - - +
1250B G 5.6 0.2 + - - -
1251B C 4.1 14.8 + - - +
1252B G 4.0 14.1 + - - +
8Q ILE* 2.8 17.0 + - + +
9Q ALA* 2.8 18.1 + - - +
11Q ALA* 1.3 77.8 - - - +
13Q HIS* 1.3 89.1 + - + +
15Q LYS* 3.4 31.1 + - - +
16Q ILE* 4.1 11.0 - - - +
31Q TYR* 5.2 2.2 - - - +
35Q PHE* 4.0 21.4 - - - -
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Residues in contact with HIS 13 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1252B G 3.8 11.0 + - - -
9Q ALA 3.4 4.6 + - - -
10Q ARG 4.8 1.3 - - - +
12Q ARG* 1.3 100.8 + - + +
14Q LYS* 1.3 56.3 + - - +
15Q LYS 2.9 2.7 - - - -
16Q ILE* 2.6 48.1 + - + +
17Q LEU* 2.8 15.1 + - + +
31Q TYR* 2.9 89.1 + + + -
32Q ARG* 4.6 1.8 - - - -
35Q PHE* 3.4 26.8 - + - -
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Residues in contact with LYS 14 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513B A 4.8 2.0 + - - -
514B A 5.0 11.5 + - - -
1217B U 2.7 46.3 + - - +
1218B G 3.1 31.6 + - - +
10Q ARG* 3.0 27.0 + - + +
11Q ALA* 2.9 13.4 + - - +
13Q HIS* 1.3 77.1 - - - +
15Q LYS* 1.3 51.3 + - - +
17Q LEU* 4.1 16.9 - - + +
18Q LYS* 2.7 38.6 + - + +
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Residues in contact with LYS 15 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1226B A 5.2 7.9 - - - +
1227B G 3.0 50.7 + - + +
8Q ILE 5.2 0.2 + - - -
11Q ALA* 3.2 14.3 + - - +
12Q ARG* 3.5 35.0 - - - +
13Q HIS 2.9 0.2 - - - -
14Q LYS* 1.3 77.5 - - - +
16Q ILE* 1.3 62.1 + - + +
18Q LYS* 3.6 6.3 - - - +
19Q GLN* 3.2 31.0 + - - +
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Residues in contact with ILE 16 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Q ARG* 4.1 13.5 - - - +
13Q HIS* 2.6 60.0 + - + +
15Q LYS* 1.3 75.0 - - + +
17Q LEU* 1.3 67.3 + - + +
18Q LYS 3.1 1.8 - - - -
19Q GLN* 3.5 8.4 + - - +
20Q ALA* 3.4 16.8 + - - +
31Q TYR 3.4 4.7 - - - +
34Q ALA* 3.4 14.1 - - + +
35Q PHE* 3.3 42.6 - - + +
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Residues in contact with LEU 17 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514B A 5.3 14.4 - - - +
515B A 5.6 2.0 - - - +
582B A 6.0 0.4 - - - +
13Q HIS* 2.8 40.6 + - + +
14Q LYS* 3.8 17.7 - - + +
16Q ILE* 1.3 90.1 - - + +
18Q LYS* 1.3 60.5 + - - +
20Q ALA* 2.9 25.9 - - + +
28Q SER 5.2 8.4 - - - +
29Q ARG 4.9 5.2 - - - +
30Q VAL 3.8 18.6 - - - +
31Q TYR* 4.3 15.9 - - + -
34Q ALA* 4.5 6.1 - - + -
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Residues in contact with LYS 18 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1218B G 5.7 5.2 - - - +
1219B U 2.9 39.7 + - - +
1220B G 5.5 5.1 + - - -
14Q LYS* 2.7 19.3 + - + +
15Q LYS* 3.6 8.1 - - - +
16Q ILE 3.1 0.2 - - - -
17Q LEU* 1.3 76.7 - - - +
19Q GLN* 1.3 81.6 + - - +
20Q ALA* 2.9 9.2 + - - +
21Q LYS* 4.1 4.3 + - - +
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Residues in contact with GLN 19 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Q LYS* 3.2 17.4 + - - +
16Q ILE* 3.5 9.3 - - - +
17Q LEU 3.4 0.2 - - - -
18Q LYS* 1.3 109.7 + - - +
20Q ALA* 1.3 55.6 + - - +
21Q LYS* 2.9 21.5 + - + +
23Q TYR* 3.8 15.6 + - - -
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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