Contacts of the helix formed by residues 33 - 45 (chain B) in PDB entry 3CJR
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 ASN 33 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A TRP* 5.0 11.2 + - - +
27B LEU* 4.9 0.2 - - - -
31B GLY 3.9 1.4 + - - -
32B ALA* 1.3 68.6 - - - +
34B ILE* 1.3 63.9 + - - +
35B MET* 3.4 9.5 + - - +
36B GLU* 3.1 46.0 + - - +
37B PHE* 3.1 18.9 + - - +
63B ARG 4.4 3.6 + - - -
65B PHE* 3.7 10.5 - - + -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A LEU* 4.7 17.7 - - - +
19B PRO* 3.7 37.0 - - + +
23B VAL* 3.9 14.4 - - + +
24B GLY* 3.5 29.8 - - - +
27B LEU* 4.3 12.8 - - + -
28B GLY* 4.1 15.0 - - - +
32B ALA 3.1 10.2 + - - +
33B ASN* 1.3 72.1 + - - +
35B MET* 1.3 61.0 + - + +
37B PHE* 3.2 3.8 + - - +
38B VAL* 2.9 32.5 + - + +
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Residues in contact with MET 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A TRP* 4.1 43.1 - - + +
97A MET 6.2 0.2 - - - +
99A PHE* 5.7 10.0 - - + -
101A THR* 6.0 1.1 - - - +
104A HIS* 5.0 2.1 - - - -
19B PRO* 4.0 36.8 - - + -
33B ASN* 3.4 7.2 + - - +
34B ILE* 1.3 77.6 - - + +
36B GLU* 1.3 61.2 + - - +
38B VAL* 3.8 11.8 - - + +
39B ALA* 3.1 26.3 + - - +
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Residues in contact with GLU 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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104A HIS* 5.1 10.0 + - + +
105A GLU* 4.6 17.5 - - - +
246A GLU* 5.6 3.4 - - - +
247A TRP* 5.4 2.6 - - - +
33B ASN* 3.1 41.2 + - - +
35B MET* 1.3 76.9 - - - +
37B PHE* 1.3 62.6 + - - +
39B ALA* 3.9 4.2 - - - +
40B ALA* 3.1 25.1 + - + +
65B PHE* 3.8 20.3 - - + -
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Residues in contact with PHE 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.7 4.0 - - + -
12B LEU* 3.9 22.4 - - + -
17B ALA* 5.2 1.1 - - + -
23B VAL* 3.7 26.7 - - + -
27B LEU* 3.5 25.1 - - + -
33B ASN 3.1 7.3 + - - +
34B ILE 3.2 4.5 + - - +
36B GLU* 1.3 73.3 - - - +
38B VAL* 1.3 60.2 + - - +
40B ALA* 3.2 1.8 + - - +
41B PHE* 2.7 62.0 + + + +
55B VAL* 4.3 2.9 - - + -
57B ILE* 3.5 35.0 - - + -
65B PHE* 3.4 19.2 - + + -
67B PHE* 3.8 30.7 - + + -
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Residues in contact with VAL 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 6.6 0.4 - - + -
17B ALA* 3.3 26.2 - - + +
18B THR* 3.6 31.9 - - - +
19B PRO* 3.7 12.3 - - + -
23B VAL* 4.0 12.6 - - + -
34B ILE* 2.9 22.1 + - + +
35B MET* 3.8 15.7 - - + +
37B PHE* 1.3 78.4 - - + +
39B ALA* 1.3 62.9 + - - +
41B PHE* 4.1 2.1 - - - +
42B ASN* 3.1 36.2 + - - +
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Residues in contact with ALA 39 (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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99A PHE* 4.0 20.2 - - + -
104A HIS* 3.4 33.9 - - + +
247A TRP* 3.7 4.5 - - + -
35B MET 3.1 18.1 + - - +
36B GLU 3.9 1.8 - - - +
38B VAL* 1.3 77.8 - - - +
40B ALA* 1.3 61.8 + - - +
42B ASN* 3.6 5.1 + - - +
43B ALA* 3.2 23.4 + - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 4.4 4.3 - - + +
246A GLU* 3.8 23.8 - - - +
247A TRP* 3.8 13.5 - - + -
36B GLU* 3.1 20.2 + - + +
37B PHE* 3.8 1.8 - - - +
39B ALA* 1.3 75.6 - - - +
41B PHE* 1.3 65.2 + - - +
43B ALA* 3.5 1.7 + - - +
44B ALA* 3.0 25.3 + - - +
65B PHE* 5.3 2.9 - - + -
67B PHE* 3.7 20.8 - - + -
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Residues in contact with PHE 41 (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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12B LEU* 3.7 24.2 - - + -
13B PRO 3.6 21.1 - - - -
17B ALA* 3.6 19.7 - - + -
37B PHE* 2.7 48.8 + + + +
38B VAL* 4.1 2.7 - - - +
40B ALA* 1.3 73.3 - - - +
42B ASN* 1.3 63.8 + - - +
44B ALA* 3.2 1.4 + - - +
45B THR* 2.9 58.5 + - + +
53B VAL* 3.9 19.1 - - + -
55B VAL* 3.8 30.3 - - + -
67B PHE* 3.6 14.5 - + - -
69B THR* 4.0 1.8 - - + -
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Residues in contact with ASN 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY* 3.5 24.9 + - - +
16B LYS* 3.2 6.0 + - - +
17B ALA* 2.8 49.6 + - - +
38B VAL* 3.1 24.5 + - - +
39B ALA* 3.9 5.3 - - - +
41B PHE* 1.3 79.2 - - - +
43B ALA* 1.3 58.1 + - - +
46B ALA* 3.1 29.1 + - - +
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Residues in contact with ALA 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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192A LEU 5.7 0.4 - - - +
193A TYR* 4.8 9.5 - - + +
195A GLU* 4.4 2.9 - - - +
218A GLY 4.5 8.1 - - - +
220A LEU* 3.8 11.6 - - + +
223A ARG* 3.5 11.3 + - - +
247A TRP* 3.6 37.0 - - + -
39B ALA 3.2 6.1 + - - +
40B ALA 3.9 0.7 - - - +
42B ASN* 1.3 77.0 - - - +
44B ALA* 1.3 64.1 + - - +
45B THR 3.4 0.5 + - - -
46B ALA* 3.5 17.9 + - - +
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Residues in contact with ALA 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A LEU* 3.7 10.1 - - + +
223A ARG* 2.8 34.9 + - - +
40B ALA 3.0 18.8 + - - +
41B PHE 3.2 4.7 + - - +
43B ALA* 1.3 76.1 - - - +
45B THR* 1.3 63.2 + - + +
46B ALA 3.5 0.4 - - - -
48B MET* 4.9 3.8 - - - +
67B PHE* 4.3 18.8 - - + -
69B THR* 5.1 5.8 + - + +
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Residues in contact with THR 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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14B ALA* 3.4 24.7 - - - +
15B GLY* 2.8 28.4 + - - -
41B PHE* 2.9 47.9 + - + +
44B ALA* 1.3 80.3 - - + +
46B ALA* 1.3 63.5 + - - +
47B ASN 3.4 2.7 - - - -
48B MET* 3.3 25.2 + - - +
53B VAL* 4.0 8.7 - - + -
69B THR* 3.8 18.4 - - + -
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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