Contacts of the helix formed by residues 22 - 29 (chain B) in PDB entry 3CJS
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A GLY* 3.9 34.1 - - - +
28A LEU 4.2 7.0 - - - +
29A TRP* 3.9 16.9 - - + -
38A PHE* 3.7 31.2 - - + -
10B LEU* 4.1 7.2 - - + -
12B LEU* 4.1 13.9 - - + -
21B PRO* 1.3 85.8 - - + +
23B VAL* 1.3 65.8 + - - +
24B GLY 3.5 0.2 - - - -
25B PRO* 3.4 3.4 - - + +
26B ALA* 3.0 27.8 + - - +
74B EDO 4.0 8.1 - - - -
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Residues in contact with VAL 23 (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 LEU* 4.1 11.9 - - + -
12B LEU* 3.8 29.6 - - + -
17B ALA* 5.0 2.2 - - + -
18B THR 3.6 12.8 - - - +
20B ALA 3.1 9.3 + - - +
22B PRO* 1.3 75.7 - - - +
24B GLY* 1.3 65.1 + - - +
26B ALA* 4.7 0.9 - - - -
27B LEU* 3.0 31.5 + - + +
34B ILE* 4.0 11.2 - - + -
37B PHE* 3.8 25.1 - - + -
38B VAL* 4.0 9.6 - - + -
74B EDO 3.4 20.6 - - - +
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Residues in contact with GLY 24 (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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56A ASP 5.1 1.1 - - - -
59A TRP* 5.0 0.7 + - - -
19B PRO 3.1 24.1 + - - -
20B ALA 3.3 0.4 + - - -
23B VAL* 1.3 77.1 - - - +
25B PRO* 1.3 64.5 - - - +
28B GLY* 2.8 30.8 + - - -
34B ILE* 3.6 19.7 - - - +
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Residues in contact with PRO 25 (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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29A TRP* 4.5 13.0 - - + -
38A PHE* 5.1 3.8 - - + -
55A GLY 5.5 3.4 - - - +
56A ASP 3.9 19.9 - - - +
59A TRP* 4.3 15.9 - - + +
21B PRO* 3.6 35.0 - - + -
22B PRO* 3.4 11.9 - - + +
24B GLY* 1.3 88.3 - - - +
26B ALA* 1.3 63.3 + - - +
29B GLN* 3.1 30.7 + - - +
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Residues in contact with ALA 26 (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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29A TRP* 3.6 34.3 - - + -
8B VAL* 3.6 32.4 - - + +
10B LEU* 4.6 2.2 - - + -
22B PRO 3.0 22.0 + - - +
23B VAL* 4.1 1.8 - - - +
25B PRO* 1.3 79.2 - - - +
27B LEU* 1.3 64.6 + - + +
29B GLN* 3.8 3.3 + - - +
30B HIS* 3.7 19.1 + - - -
59B ILE* 4.1 0.2 - - - +
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Residues in contact with LEU 27 (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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8B VAL* 4.4 5.2 - - + -
10B LEU* 4.9 2.2 - - + -
23B VAL* 3.0 25.4 + - + +
26B ALA* 1.3 87.8 - - + +
28B GLY* 1.3 64.9 + - - +
29B GLN 3.3 0.7 - - - -
30B HIS* 3.1 14.7 + - - +
32B ALA* 3.2 43.6 + - + +
33B ASN 4.6 4.5 - - - +
34B ILE* 4.4 6.5 - - + -
37B PHE* 3.4 42.0 - - + -
57B ILE* 4.3 34.1 - - + -
59B ILE* 3.9 9.2 - - + -
65B PHE* 5.1 1.6 - - + -
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Residues in contact with GLY 28 (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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59A TRP* 3.5 22.1 - - - -
24B GLY 2.8 24.2 + - - -
27B LEU* 1.3 73.4 - - - +
29B GLN* 1.3 61.8 + - - +
31B GLY* 2.9 15.4 + - - -
32B ALA 4.4 3.6 - - - -
34B ILE* 4.1 16.3 - - - +
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Residues in contact with GLN 29 (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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29A TRP* 4.1 27.0 - - - -
31A ARG* 4.4 10.3 + - - +
59A TRP* 3.5 52.5 - - + +
8B VAL* 6.2 0.2 - - - +
25B PRO 3.1 20.2 + - - +
26B ALA 3.8 3.0 + - - +
28B GLY* 1.3 75.2 - - - +
30B HIS* 1.3 93.4 + - + +
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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