Contacts of the helix formed by residues 34 - 43 (chain C) in PDB entry 2P2N
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 GLN 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C LEU* 1.3 73.8 + - + +
36C ALA* 3.2 7.7 - - - +
37C LEU* 3.2 28.5 + - - +
38C MET* 3.0 26.2 - - + +
121C LEU* 3.6 28.1 - - + +
122C ALA* 3.6 27.5 - - - +
129C GLN* 5.0 1.6 - - - +
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Residues in contact with LEU 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 1.3 82.9 - - + +
36C ALA* 1.3 59.8 + - - +
38C MET* 3.0 38.6 + - + +
41C PHE* 3.7 46.3 - - + +
42C HIS* 3.5 12.5 + - + +
49C PHE* 5.0 6.1 - - + -
51C ILE* 4.1 27.8 - - + -
129C GLN* 5.1 4.7 - - + +
132C LEU* 4.1 14.4 - - + -
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN 4.2 4.9 - - - +
35C LEU* 1.3 78.1 - - - +
37C LEU* 1.3 60.6 + - + +
38C MET 3.2 7.1 + - - +
39C PRO* 5.5 0.5 - - - +
42C HIS* 4.0 16.2 + - + +
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Residues in contact with LEU 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 3.2 18.3 + - + +
35C LEU 3.2 1.2 - - - -
36C ALA* 1.3 80.1 - - + +
38C MET* 1.3 59.8 + - + +
39C PRO* 4.1 4.8 - - - +
37D LEU 4.2 2.8 - - - +
39D PRO* 3.7 45.3 - - + +
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Residues in contact with MET 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C GLN* 3.0 42.4 - - + +
35C LEU* 3.0 31.5 + - + +
36C ALA 3.2 3.2 - - - -
37C LEU* 1.3 84.0 - - + +
39C PRO* 1.4 70.1 - - + +
40C GLU* 3.4 9.8 + - + +
41C PHE* 3.8 17.7 + - + +
42C HIS* 3.7 10.2 - - - -
129C GLN* 3.2 40.4 - - + +
39D PRO* 5.3 7.2 - - + -
40D GLU* 6.1 0.7 - - - +
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Residues in contact with PRO 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ALA 5.5 1.1 - - - +
37C LEU 4.1 5.6 - - - +
38C MET* 1.4 81.4 - - + +
40C GLU* 1.3 68.6 + - + +
41C PHE 3.2 2.5 - - - -
42C HIS* 3.3 18.7 + - + +
43C ARG* 3.5 13.5 + - - +
34D GLN* 5.0 11.7 - - - +
37D LEU* 4.5 24.0 - - + +
38D MET* 5.4 11.7 - - + -
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Residues in contact with GLU 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C MET* 4.7 10.6 - - + +
39C PRO* 1.3 83.6 - - + +
41C PHE* 1.3 86.6 + - + +
43C ARG* 3.2 28.9 + - + +
46C MET* 3.7 0.9 - - - +
129C GLN* 4.3 13.2 - - - +
130C ILE* 5.4 5.5 + - - +
133C LEU* 4.0 22.2 - - + +
38D MET* 6.5 0.2 - - + -
123D GLU 5.6 4.7 - - - +
124D LEU* 3.6 17.1 - - + +
125D ARG 5.1 4.5 + - - -
126D SER* 5.4 3.3 + - - +
129D GLN* 3.5 33.0 + - - +
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Residues in contact with PHE 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C LEU* 3.7 28.0 - - + +
38C MET* 4.0 19.3 - - + +
39C PRO 3.2 1.0 - - - -
40C GLU* 1.3 104.0 - - + +
42C HIS* 1.3 65.7 + - + +
43C ARG 3.5 0.4 - - - -
46C MET* 3.5 21.1 - - + +
47C PRO 4.9 0.5 - - - +
49C PHE* 3.6 40.0 - + + -
129C GLN* 3.3 39.5 - - + -
132C LEU* 3.8 26.5 - - + -
133C LEU* 3.9 23.1 - - + -
136C LEU* 4.1 8.1 - - + -
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Residues in contact with HIS 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 5.8 0.7 + - - -
35C LEU* 3.5 19.2 + - + -
36C ALA* 4.0 14.6 - - - +
38C MET 3.7 18.6 - - - -
39C PRO* 3.3 10.1 + - + +
40C GLU 3.2 0.8 - - - -
41C PHE* 1.3 78.8 + - + +
43C ARG* 1.3 67.0 + - - +
44C PRO* 3.8 1.6 - - - +
49C PHE* 4.5 20.1 - + - -
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Residues in contact with ARG 43 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LYS* 4.9 2.6 + - - -
39C PRO 3.5 13.7 + - - +
40C GLU* 3.2 27.0 + - - +
41C PHE 3.5 0.4 - - - -
42C HIS* 1.3 82.2 - - - +
44C PRO* 1.4 74.7 - - + +
45C GLU* 2.7 31.9 + - - +
46C MET* 3.2 17.8 + - + +
122D ALA* 2.6 32.5 + - - +
123D GLU* 3.5 11.3 + - - +
124D LEU* 3.1 41.0 - - + +
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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