Contacts of the helix formed by residues 22 - 29 (chain H) in PDB entry 3CJQ
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 22 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26G ARG 4.8 1.6 - - - +
27G GLY* 3.9 24.7 - - - +
28G LEU 3.6 25.8 - - - +
29G TRP* 3.9 18.5 - - + -
38G PHE* 4.4 8.9 - - + -
10H LEU* 3.9 13.5 - - + -
12H LEU* 3.8 23.6 - - + -
20H ALA 4.1 0.7 - - - +
21H PRO* 1.4 84.2 - - + +
23H VAL* 1.3 66.0 + - + +
25H PRO* 3.4 3.3 - - - +
26H ALA* 3.0 27.5 + - - +
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Residues in contact with VAL 23 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10H LEU* 4.1 12.6 - - + -
12H LEU* 4.0 26.2 - - + -
17H ALA* 4.8 1.6 - - + -
18H THR 3.2 29.2 - - - +
20H ALA 2.9 4.9 + - - +
22H PRO* 1.3 75.7 - - + +
24H GLY* 1.3 65.9 + - - +
26H ALA* 3.0 13.6 + - - -
27H LEU* 3.1 26.0 + - + +
28H GLY 3.8 0.2 + - - -
34H ILE* 3.9 20.1 - - + +
37H PHE* 3.8 31.6 - - + -
38H VAL* 4.6 3.1 - - + -
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Residues in contact with GLY 24 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G TRP* 4.0 18.0 - - - +
19H PRO 3.3 23.1 + - - -
20H ALA 3.0 10.8 + - - -
23H VAL* 1.3 78.5 - - - +
25H PRO* 1.3 63.5 - - - +
28H GLY* 3.2 22.7 + - - -
34H ILE* 3.4 12.1 - - - +
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Residues in contact with PRO 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TRP* 3.5 26.2 - - + -
38G PHE* 5.4 1.6 - - + -
59G TRP* 4.7 11.0 - - + +
21H PRO* 3.5 31.9 - - + -
22H PRO 3.4 11.7 - - - +
24H GLY* 1.3 89.7 - - - +
26H ALA* 1.3 60.7 + - - +
28H GLY 5.2 0.2 - - - -
29H GLN* 2.8 36.8 + - + +
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Residues in contact with ALA 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TRP* 3.6 32.4 - - + -
8H VAL* 3.9 28.1 - - + +
10H LEU* 4.2 5.2 - - + -
22H PRO 3.0 26.9 + - - +
23H VAL 3.0 1.3 + - - +
25H PRO* 1.3 74.1 - - - +
27H LEU* 1.3 64.6 + - + +
29H GLN* 4.3 2.5 + - - +
30H HIS* 3.6 21.5 + - - -
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H VAL* 5.1 1.1 - - + -
10H LEU* 4.6 2.5 - - + -
23H VAL* 3.1 27.8 + - + +
26H ALA* 1.3 83.1 - - + +
28H GLY* 1.4 57.8 + - - +
29H GLN 3.2 2.2 - - - -
30H HIS* 2.8 26.7 + - - +
31H GLY 3.1 7.8 + - - -
32H ALA* 3.5 25.6 + - + -
33H ASN 4.8 2.7 - - - +
34H ILE* 4.6 8.5 - - + -
37H PHE* 3.8 31.4 - - + -
57H ILE* 3.8 49.8 - - + -
59H ILE* 4.1 10.3 - - + -
65H PHE* 4.6 5.4 - - + -
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Residues in contact with GLY 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59G TRP* 6.0 0.2 - - - -
63G TRP* 4.9 8.2 - - - +
23H VAL 3.8 0.2 + - - -
24H GLY 3.2 21.2 + - - -
25H PRO 3.2 2.2 + - - -
27H LEU* 1.4 77.7 - - - +
29H GLN* 1.3 55.9 + - - +
31H GLY* 3.0 20.3 + - - -
32H ALA 4.6 2.9 - - - -
34H ILE* 3.8 18.2 - - - +
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Residues in contact with GLN 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G TRP* 5.0 8.3 - - - -
31G ARG* 4.0 21.6 + - - +
25H PRO* 2.8 21.1 + - + +
26H ALA 4.3 3.2 + - - +
27H LEU 3.1 0.2 + - - -
28H GLY* 1.3 70.9 - - - +
30H HIS* 1.3 88.0 + - + +
31H GLY 3.4 0.4 + - - -
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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