Contacts of the helix formed by residues 42 - 50 (chain B) in PDB entry 2NP5
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 42 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ALA* 4.5 0.7 - - - -
40B GLY 3.8 1.8 + - - -
41B VAL* 1.3 78.2 - - - +
43B ILE* 1.3 65.8 + - - +
44B GLY* 4.1 3.2 + - - -
45B ALA* 3.0 41.8 + - - +
46B VAL* 3.4 6.4 + - - +
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Residues in contact with ILE 43 (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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32B VAL* 4.8 16.2 - - + -
33B ARG* 4.7 24.9 - - + +
36B ALA* 4.2 9.4 - - + -
41B VAL 3.8 1.0 + - - +
42B SER* 1.3 76.3 - - - +
44B GLY* 1.3 60.7 + - - +
46B VAL* 3.3 24.2 + - - +
47B GLN* 3.4 16.4 - - - +
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Residues in contact with GLY 44 (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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42B SER* 3.2 3.9 + - - -
43B ILE* 1.3 78.9 - - - +
45B ALA* 1.3 61.2 + - - +
47B GLN* 3.2 21.5 + - - +
48B HIS* 3.1 19.8 + - - +
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Residues in contact with ALA 45 (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 SER* 4.9 4.7 - - - +
14B LEU* 4.8 0.7 - - - +
41B VAL* 3.5 19.7 - - + +
42B SER* 3.0 27.6 + - - +
44B GLY* 1.3 73.7 - - - +
46B VAL* 1.3 63.1 - - - +
48B HIS* 3.5 8.9 + - + +
49B HIS* 3.2 32.1 + - + +
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Residues in contact with VAL 46 (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 LEU* 3.9 27.1 - - + -
32B VAL* 3.8 26.7 - - + +
36B ALA* 3.6 29.4 - - + -
41B VAL* 5.0 0.7 - - + -
42B SER 3.7 4.7 - - - +
43B ILE* 3.4 13.2 - - - +
44B GLY 3.1 0.4 - - - -
45B ALA* 1.3 77.9 - - - +
47B GLN* 1.3 59.1 + - + +
49B HIS* 3.1 4.5 + - - +
50B PHE* 2.8 34.9 + - + +
56B MSE 4.0 21.8 - - + -
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Residues in contact with GLN 47 (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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43B ILE* 3.4 20.0 + - + +
44B GLY* 3.2 17.7 + - - +
46B VAL* 1.3 76.4 - - + +
48B HIS* 1.3 61.9 + - - +
50B PHE 3.4 21.1 + - - +
51B SER* 4.6 1.7 + - - -
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Residues in contact with HIS 48 (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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44B GLY 3.1 11.4 + - - +
45B ALA* 3.7 14.1 - - + +
46B VAL 3.2 0.4 - - - -
47B GLN* 1.3 79.2 - - - +
49B HIS* 1.3 87.6 + + - +
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Residues in contact with HIS 49 (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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9B THR* 4.7 5.5 + - - -
10B SER* 3.6 30.8 - - - -
11B PRO* 3.5 31.3 - - + +
14B LEU* 5.0 1.5 - - + +
45B ALA* 3.2 21.0 + - + +
46B VAL 3.1 6.0 + - - +
48B HIS* 1.3 103.1 + + + +
50B PHE* 1.3 72.7 + - + +
51B SER 4.3 0.6 + - - -
55B GLU* 3.4 13.3 - - - +
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Residues in contact with PHE 50 (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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11B PRO* 3.9 19.5 - - + -
14B LEU* 3.6 33.9 - - + -
15B ALA 5.7 0.2 - - - -
46B VAL* 2.8 24.4 + - + +
47B GLN* 3.4 18.3 - - - +
48B HIS 3.6 0.2 - - - -
49B HIS* 1.3 86.4 - - + +
51B SER* 1.3 67.5 + - - +
52B THR* 3.9 16.2 - - - +
55B GLU* 3.6 22.2 - - + -
56B MSE 3.8 30.5 - - + +
59B PHE* 3.6 48.5 - + + -
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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