Contacts of the helix formed by residues 26 - 36 (chain A) in PDB entry 2NPJ
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 PRO 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A PHE* 3.6 26.2 - - + -
24A THR 3.3 7.2 - - - +
25A ILE* 1.4 85.2 - - + +
27A GLY* 1.3 66.2 - - - +
29A ALA* 3.1 9.6 + - + +
30A LEU* 2.9 39.7 + - + +
207A ILE* 3.9 18.8 - - + -
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Residues in contact with GLY 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A PHE 3.1 9.1 + - - -
23A MET 3.2 10.4 + - - -
26A PRO* 1.3 78.4 - - - +
28A ILE* 1.3 57.4 + - - +
30A LEU 3.2 0.3 + - - -
31A PHE* 3.0 24.8 + - - +
204A GLY* 3.4 18.1 - - - -
207A ILE* 3.5 25.8 - - - -
208A LEU* 4.2 4.0 - - - -
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A MET 2.7 13.4 + - - +
24A THR* 3.7 30.3 - - + +
26A PRO 3.6 0.2 - - - -
27A GLY* 1.3 72.2 - - - +
29A ALA* 1.3 65.3 + - - +
31A PHE* 3.5 12.5 - - + +
32A TYR* 3.0 54.4 + - + -
48A VAL* 4.5 6.1 - - + -
110A ILE* 3.9 7.2 - - + -
113A GLY* 4.0 20.0 - - - +
114A LEU* 3.5 29.8 - - + -
208A LEU* 4.0 20.8 - - + +
314A VAL* 5.9 0.2 - - + -
318A PHE* 5.2 3.6 - - + -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A THR 3.8 8.5 + - - +
25A ILE* 5.8 1.8 - - + -
26A PRO* 3.1 13.4 + - + +
28A ILE* 1.3 83.1 - - - +
30A LEU* 1.3 59.0 + - + +
33A GLY* 2.8 25.8 + - - -
44A MET* 3.4 15.1 - - - +
45A LEU* 3.6 24.3 - - + +
48A VAL* 4.2 18.8 - - + -
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 2.9 30.7 + - + +
27A GLY 3.8 2.9 - - - +
29A ALA* 1.3 76.1 - - + +
31A PHE* 1.3 67.5 + - - +
33A GLY* 4.2 0.7 - - - +
34A GLY 3.1 18.9 + - - -
45A LEU* 5.4 9.0 - - + -
200A MET* 3.3 42.7 - - + +
203A THR* 4.2 15.0 - - + -
204A GLY* 3.9 8.1 - - - -
207A ILE* 3.9 28.0 - - + -
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Residues in contact with PHE 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLY 3.0 12.9 + - - +
28A ILE* 3.5 26.2 - - + +
30A LEU* 1.3 78.2 - - - +
32A TYR* 1.3 69.1 + + - +
34A GLY 3.5 5.7 + - - -
35A LEU* 3.5 41.3 + - + +
201A VAL* 3.7 25.0 - - + +
204A GLY* 3.8 6.2 - - - -
205A THR* 3.3 31.2 - - - -
208A LEU* 4.1 13.0 - - + -
259A LEU* 5.7 3.6 - - + -
262A CYS* 5.0 4.0 - - + -
263A SER* 5.7 5.4 - - - -
266A ILE* 4.2 22.2 - - + -
314A VAL* 3.8 24.9 - - + -
318A PHE* 5.7 1.6 - + - -
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Residues in contact with TYR 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ILE* 3.0 49.5 + - + +
31A PHE* 1.3 76.1 - + - +
33A GLY* 1.3 66.0 + - - +
35A LEU* 3.0 18.7 + - + -
36A ILE* 3.0 20.6 + - + +
44A MET* 3.9 11.4 - - + -
113A GLY 4.0 0.2 - - - -
114A LEU* 2.7 31.6 + - - +
117A GLY* 3.3 33.4 - - - +
118A ALA* 3.4 27.6 - - + +
311A PRO* 3.9 24.2 - - + -
314A VAL* 3.4 30.2 - - + +
315A PHE* 3.8 3.8 - - - -
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Residues in contact with GLY 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ALA 2.8 20.2 + - - -
30A LEU 3.2 3.1 + - - -
32A TYR* 1.3 77.8 - - - +
34A GLY* 1.3 55.4 + - - +
36A ILE* 4.0 1.6 - - - +
41A VAL* 3.4 15.4 - - - +
44A MET* 3.4 14.3 - - - +
45A LEU* 5.3 1.1 - - - -
196A HIS* 2.9 24.6 + - - -
200A MET* 3.5 14.6 - - - +
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Residues in contact with GLY 34 (chain A).
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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30A LEU 3.1 10.3 + - - -
31A PHE 3.5 0.2 + - - -
32A TYR 3.2 0.4 - - - -
33A GLY* 1.3 76.1 - - - +
35A LEU* 1.3 58.5 + - - +
195A PRO* 3.4 6.8 - - - +
196A HIS* 3.4 12.2 + - - -
197A ASN* 3.3 45.4 + - - -
200A MET* 3.6 5.3 - - - -
201A VAL* 3.4 12.9 - - - +
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Residues in contact with LEU 35 (chain A).
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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31A PHE* 3.5 45.1 + - + +
32A TYR* 3.0 15.1 + - + +
34A GLY* 1.3 77.8 - - - +
36A ILE* 1.3 63.7 + - - +
195A PRO* 3.8 40.9 - - + +
196A HIS 4.9 0.2 + - - -
201A VAL* 3.8 9.0 - - + -
259A LEU* 3.8 23.6 - - + -
311A PRO* 4.6 16.5 - - + +
314A VAL* 3.9 16.8 - - + -
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Residues in contact with ILE 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A TYR* 3.0 18.5 + - + +
33A GLY 4.2 0.2 - - - +
34A GLY 3.7 0.2 - - - -
35A LEU* 1.3 78.3 - - - +
37A ARG* 1.3 62.5 + - - +
40A ASN* 3.7 22.4 - - + +
41A VAL* 3.9 9.4 - - + -
44A MET* 3.6 42.2 - - + -
117A GLY 4.6 7.9 - - - +
118A ALA 5.2 0.2 - - - +
121A GLU* 3.6 20.2 - - + +
196A HIS* 2.7 36.1 + - - -
311A PRO* 3.6 34.5 - - + -
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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