Contacts of the helix formed by residues 19 - 29 (chain M) in PDB entry 1JJ2
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 ASP 19 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23680 A 3.7 34.8 - - - +
23690 A 4.5 4.6 + - - -
17M ARG 4.3 0.8 + - - -
18M THR* 1.3 73.8 - - - +
20M TYR* 1.3 56.0 + - - +
21M HIS* 2.9 12.1 + - - +
22M GLN* 2.7 40.1 + - + +
23M ARG* 3.0 23.6 + - - +
25M ARG* 5.5 1.1 + - - -
105M GLY* 5.3 2.0 - - - +
106M LEU* 3.9 21.8 - - + +
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Residues in contact with TYR 20 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23680 A 4.7 2.6 + - - -
79 G 4.9 0.2 - - - -
89 G 2.7 38.5 + - - -
109 C 3.6 11.6 + - - -
10M MET* 3.5 33.0 - - + -
12M ARG* 3.4 24.8 + - + +
13M ARG* 4.3 15.0 - - + +
18M THR* 3.3 35.4 + - + +
19M ASP* 1.3 70.7 + - - +
21M HIS* 1.3 66.0 + - + +
23M ARG* 3.8 7.9 - - - +
24M LEU* 3.2 22.7 + - - +
23P THR* 5.4 10.7 - - + +
24P SER 5.7 0.2 - - - +
26P PRO* 3.5 33.0 - - + +
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Residues in contact with HIS 21 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23660 C 5.6 0.2 + - - -
23670 A 5.1 1.4 - - - -
23680 A 5.0 9.6 - + - -
23690 A 3.5 49.8 + - - +
23700 A 4.8 16.8 + - - -
19M ASP* 2.9 7.4 + - - +
20M TYR* 1.3 80.1 - - + +
22M GLN* 1.3 63.2 + - - +
24M LEU* 3.6 6.9 + - - +
25M ARG* 3.4 42.2 + - - +
23P THR* 3.2 38.3 + - + +
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Residues in contact with GLN 22 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24130 A 3.8 24.0 + - - +
24140 A 4.2 7.6 + - - -
24150 A 3.7 7.4 - - + -
19M ASP* 2.7 32.0 + - - +
21M HIS* 1.3 72.9 - - - +
23M ARG* 1.3 58.8 + - - +
25M ARG* 3.3 27.5 + - - +
26M LEU* 2.9 45.4 + - + +
103M ASP* 4.3 0.9 - - - +
104M ILE* 4.7 6.1 - - - +
105M GLY* 3.2 33.8 + - - +
107M ASN 5.9 0.2 + - - -
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Residues in contact with ARG 23 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79 G 2.8 41.7 + - - -
89 G 2.8 27.2 + - - -
18M THR* 4.1 11.4 - - + -
19M ASP 3.0 17.2 + - - +
20M TYR* 3.8 11.4 - - - +
21M HIS 3.3 0.2 - - - -
22M GLN* 1.3 77.7 - - - +
24M LEU* 1.3 59.0 + - - +
26M LEU* 2.9 13.6 + - + +
27M LEU* 2.8 53.2 + - + +
33M ARG* 3.8 14.1 - - - +
50M LEU* 3.5 13.9 - - - +
55M ASP* 2.8 36.0 + - - -
103M ASP* 5.8 0.9 - - - +
26P PRO* 4.6 8.8 - - + +
27P GLN* 4.6 6.1 + - - +
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Residues in contact with LEU 24 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M TYR 3.2 13.9 + - - +
21M HIS* 3.9 8.3 - - - +
22M GLN 3.3 0.2 - - - -
23M ARG* 1.3 77.8 - - - +
25M ARG* 1.3 65.6 + - + +
27M LEU* 3.1 12.5 + - - +
28M LYS* 3.1 37.8 + - + +
26P PRO* 4.0 22.4 - - + +
29P ALA* 4.2 17.3 - - + +
30P VAL* 3.7 26.5 - - + -
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Residues in contact with ARG 25 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23260 U 5.9 1.3 + - - -
23270 A 5.7 3.0 + - - -
23690 A 4.9 5.3 + - - -
24140 A 5.0 2.2 + - - +
24150 A 2.9 66.9 + - + +
24160 G 3.2 28.8 - - - +
24170 C 5.4 3.1 - - - -
19M ASP* 5.5 1.0 + - - -
21M HIS* 3.4 33.4 + - - +
22M GLN* 3.3 29.8 + - - +
23M ARG 3.3 0.6 - - - -
24M LEU* 1.3 78.7 - - + +
26M LEU* 1.3 57.2 + - - +
28M LYS* 3.2 22.4 - - + +
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Residues in contact with LEU 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24140 A 4.8 4.0 - - + -
24150 A 2.9 36.9 + - + +
22M GLN* 2.9 37.8 + - + +
23M ARG* 2.9 12.3 + - - +
25M ARG* 1.3 77.8 - - - +
27M LEU* 1.3 58.5 + - - +
28M LYS 3.0 2.6 + - - -
29M SER* 3.0 13.5 + - - -
31M LYS 5.2 1.2 - - - +
33M ARG* 4.1 23.4 - - + +
101M VAL* 4.1 18.6 - - + +
102M LEU 3.9 18.4 - - - +
103M ASP* 3.6 33.9 - - + +
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Residues in contact with LEU 27 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23M ARG* 2.8 52.7 + - + +
24M LEU 3.6 7.4 - - - +
26M LEU* 1.3 69.6 - - - +
28M LYS* 1.3 64.2 + - - +
29M SER* 3.2 0.9 - - - -
30M GLY* 3.2 14.5 + - - +
31M LYS 5.6 5.6 - - - +
33M ARG* 4.2 26.5 - - + +
50M LEU* 3.8 37.0 - - + +
26P PRO* 4.7 9.4 - - + +
27P GLN* 5.3 1.6 - - - +
30P VAL* 3.8 36.6 - - + +
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Residues in contact with LYS 28 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24160 G 3.3 26.6 + - - +
24170 C 3.1 29.0 + - - +
24M LEU* 3.1 41.0 + - + +
25M ARG* 3.2 21.5 - - - +
26M LEU 3.0 0.6 + - - -
27M LEU* 1.3 79.0 - - - +
29M SER* 1.3 63.1 + - - +
30M GLY* 3.1 2.1 + - - -
30P VAL* 5.6 2.5 - - + -
69P ASP* 5.3 12.3 + - - +
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Residues in contact with SER 29 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24150 A 3.2 29.9 + - - -
24160 G 3.8 5.4 - - - -
26M LEU 3.0 12.6 + - - -
28M LYS* 1.3 78.1 - - - +
30M GLY* 1.3 62.5 + - - +
31M LYS* 2.9 30.8 + - - +
101M VAL* 3.3 24.5 - - - +
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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