Contacts of the helix formed by residues 29 - 37 (chain B) in PDB entry 2CX9
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 GLY 29 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B GLU 5.0 1.8 + - - -
26B VAL 3.4 4.2 + - - -
27B ALA 3.2 0.6 - - - -
28B PRO* 1.3 78.5 - - - +
30B ALA* 1.3 64.4 + - - +
31B ALA 3.3 2.7 - - - -
32B GLU* 3.2 16.5 + - - +
33B ARG* 3.0 41.7 + - - +
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Residues in contact with ALA 30 (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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26B VAL 4.2 1.6 - - - +
27B ALA 3.4 13.4 + - - +
29B GLY* 1.3 75.7 - - - +
31B ALA* 1.3 64.0 + - - +
33B ARG* 3.3 17.9 + - - +
34B ASP* 3.1 22.3 + - - +
81B TYR 3.2 27.8 - - - +
82B ASP* 3.5 14.6 - - - +
357B ARG* 3.6 19.0 + - - +
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Residues in contact with ALA 31 (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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27B ALA 4.9 1.4 + - - -
28B PRO 4.9 4.2 + - - +
29B GLY 3.3 0.8 - - - -
30B ALA* 1.3 76.3 - - - +
32B GLU* 1.3 62.7 + - - +
34B ASP* 3.3 16.2 + - - +
35B ARG* 3.4 34.2 + - - +
351B LYS 5.7 4.3 - - - +
357B ARG* 3.6 18.6 - - - +
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Residues in contact with GLU 32 (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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28B PRO 5.4 0.6 + - - +
29B GLY* 3.2 16.1 + - - +
31B ALA* 1.3 81.5 - - - +
33B ARG* 1.3 58.9 + - + +
35B ARG* 3.1 30.5 + - - +
36B THR* 3.0 42.5 + - + +
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Residues in contact with ARG 33 (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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25B GLU 5.0 1.6 + - - -
26B VAL* 2.8 28.9 + - - +
29B GLY* 3.0 31.0 + - - +
30B ALA* 3.3 8.3 + - - +
32B GLU* 1.3 78.5 - - + +
34B ASP* 1.3 56.0 + - - +
36B THR* 3.9 7.4 - - - +
37B GLY* 2.7 32.6 + - - +
38B ALA* 4.2 11.2 - - + +
40B PRO* 3.7 31.2 - - - +
43B LEU* 3.4 27.9 - - - +
82B ASP* 2.8 36.5 + - - +
84B ALA* 6.2 0.4 - - + -
85B LEU* 4.9 0.2 - - - +
211B THR* 3.9 0.7 - - - -
212B ALA* 3.7 17.5 - - + +
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Residues in contact with ASP 34 (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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30B ALA 3.1 6.5 + - - +
31B ALA* 3.5 10.8 - - - +
32B GLU 3.2 0.4 - - - -
33B ARG* 1.3 77.1 - - - +
35B ARG* 1.3 61.0 + - - +
211B THR* 2.7 53.1 + - - +
212B ALA 5.0 0.7 - - - +
351B LYS* 4.9 5.5 + - - +
356B GLU* 4.5 1.7 - - - +
357B ARG* 3.6 29.1 - - - +
360B ARG* 3.0 40.1 + - - -
361B ASP* 4.7 2.6 - - - +
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Residues in contact with ARG 35 (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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31B ALA* 3.5 27.8 + - - +
32B GLU* 3.1 44.7 + - - +
34B ASP* 1.3 86.4 - - - +
36B THR* 1.3 64.1 + - + +
211B THR* 4.8 3.0 - - - +
351B LYS* 5.2 8.1 + - - +
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Residues in contact with THR 36 (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 GLU* 3.0 35.7 + - + +
33B ARG* 3.9 4.9 + - - +
35B ARG* 1.3 82.3 - - + +
37B GLY* 1.3 64.3 + - - +
38B ALA* 3.1 24.2 + - - +
204B LYS* 5.5 0.3 + - - -
211B THR* 4.7 0.9 - - - -
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Residues in contact with GLY 37 (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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33B ARG 2.7 22.3 + - - -
35B ARG 3.5 1.4 - - - -
36B THR* 1.3 72.4 + - - +
38B ALA* 1.3 62.8 + - - +
39B PHE* 3.3 1.0 + - - -
204B LYS* 3.3 23.3 + - - -
211B THR* 3.6 29.1 - - - +
212B ALA* 3.7 11.4 - - - -
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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