Contacts of the helix formed by residues 23 - 31 (chain M) in PDB entry 2JA7
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 SER 23 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M LEU 3.5 2.6 + - - -
22M PHE* 1.3 74.2 - - - +
24M PRO* 1.3 70.2 - - - +
25M GLU* 3.8 11.5 + - - +
26M GLU* 2.5 40.7 + - - +
27M VAL* 3.1 7.7 + - - -
233M TRP* 2.8 42.2 - - - +
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Residues in contact with PRO 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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22M PHE 3.7 4.5 - - - +
23M SER* 1.3 80.9 - - - +
25M GLU* 1.3 79.9 + - - +
27M VAL* 3.3 6.6 + - + +
28M ARG* 3.1 31.6 + - - +
233M TRP* 3.3 21.1 - - + +
235M ILE 5.6 4.0 - - - +
237M THR* 4.0 28.3 - - + +
238M CYS* 3.8 25.2 - - + +
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Residues in contact with GLU 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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200D ASN* 6.1 0.9 - - - +
23M SER* 2.7 21.3 + - - +
24M PRO* 1.3 91.8 - - - +
26M GLU* 1.3 63.7 + - - +
28M ARG* 3.3 11.1 + - - +
29M ALA* 3.1 17.9 + - - +
233M TRP* 4.4 5.2 + - - -
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Residues in contact with GLU 26 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M LEU 5.2 0.5 - - - +
22M PHE* 3.6 30.5 - - + -
23M SER* 2.5 30.6 + - - +
25M GLU* 1.3 70.6 - - - +
27M VAL* 1.3 69.5 + - - +
29M ALA* 2.6 23.6 + - + +
30M ILE* 3.0 19.9 + - + +
1166N CYS* 4.2 6.8 - - - +
1168N LEU* 3.6 10.7 - - - +
1185N CYS* 4.6 5.2 - - - -
1213N THR* 4.8 0.2 - - - +
1215N ARG* 3.2 37.9 + - - -
15P LEU* 4.4 7.6 - - - +
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Residues in contact with VAL 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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22M PHE* 3.5 39.7 - - + -
23M SER 3.7 9.0 - - - +
24M PRO* 3.4 10.8 - - + +
26M GLU* 1.3 77.9 - - - +
28M ARG* 1.3 62.0 + - - +
30M ILE* 3.6 6.4 + - - +
31M SER* 3.1 21.7 + - - -
82M GLY 5.0 0.7 - - - +
83M HIS* 3.9 8.5 - - + -
238M CYS* 3.7 25.1 - - + +
240M PRO* 3.9 28.7 - - + -
1211N ASN* 4.2 8.5 - - - +
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Residues in contact with ARG 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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192D LYS* 5.1 7.1 - - - +
199D ASN 5.5 2.2 + - - -
203D SER* 5.9 3.0 - - - +
204D ASP* 3.1 28.5 + - - +
24M PRO* 3.1 20.1 + - - +
25M GLU* 3.5 10.5 - - - +
26M GLU 2.7 4.0 + - - -
27M VAL* 1.3 73.8 - - - +
29M ALA* 1.3 69.7 + - - +
31M SER* 3.1 18.4 + - - +
83M HIS* 4.0 18.9 - - + +
85M ASP* 3.6 18.7 + - - +
237M THR* 4.8 16.0 + - - +
238M CYS* 3.7 19.7 - - - +
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Residues in contact with ALA 29 (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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25M GLU 3.1 8.3 + - - +
26M GLU* 2.6 17.9 + - + +
28M ARG* 1.3 76.5 - - - +
30M ILE* 1.3 65.5 + - + +
31M SER 3.4 6.1 - - - +
1183N LYS* 4.5 12.2 + - - +
1184N GLY* 3.6 29.7 - - - +
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Residues in contact with ILE 30 (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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22M PHE* 3.5 36.6 - - + -
26M GLU* 3.0 16.6 + - + +
27M VAL* 3.7 9.2 - - - +
29M ALA* 1.3 81.3 - - + +
31M SER* 1.3 67.1 + - - +
32M VAL* 3.5 5.2 - - - +
81M PHE* 4.2 24.1 - - + +
1168N LEU* 3.7 22.4 - - + -
1170N THR* 3.9 28.9 - - + +
1183N LYS* 3.5 21.0 + - - +
1184N GLY* 6.1 0.9 - - - -
1185N CYS* 5.6 4.7 - - - -
1208N MET* 5.2 4.7 - - + -
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Residues in contact with SER 31 (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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27M VAL 3.1 10.1 + - - -
28M ARG 3.1 14.6 + - - +
29M ALA 3.4 8.1 - - - +
30M ILE* 1.3 84.9 - - - +
32M VAL* 1.3 62.9 + - - +
33M ALA 3.0 15.8 + - - -
81M PHE 3.3 10.1 - - - -
82M GLY* 3.0 5.4 - - - -
83M HIS* 2.9 41.4 + - - -
1183N LYS* 5.8 1.4 - - - +
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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