Contacts of the helix formed by residues 27 - 42 (chain A) in PDB entry 3JRC
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 LEU 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.2 24.6 + - + +
12A THR* 4.0 0.6 - - - +
13A VAL* 3.8 12.1 - - + -
25A LYS 3.7 1.4 + - - -
26A PRO* 1.3 71.0 - - - +
28A ARG* 1.3 58.6 + - - +
30A SER* 2.9 25.5 + - - -
31A VAL* 3.0 19.4 + - + +
27B LEU* 5.2 0.7 - - + -
30B SER* 3.6 40.2 - - - +
31B VAL* 3.8 28.7 - - + +
34B ALA* 4.0 13.7 - - + -
54B VAL* 5.4 3.8 - - + -
57B GLU* 3.8 17.4 + - + -
58B VAL* 4.6 13.5 - - + -
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Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ASP* 3.5 23.4 + - - -
26A PRO* 3.1 29.0 - - + +
27A LEU* 1.3 80.0 - - - +
29A ASP* 1.3 69.7 + - - +
31A VAL* 3.4 3.0 + - - -
32A LYS* 3.0 27.6 + - + +
57B GLU* 3.0 64.2 + - - +
60B GLN* 4.5 20.9 + - - +
61B PRO* 3.4 22.1 - - + +
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Residues in contact with ASP 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 3.9 20.8 - - + +
26A PRO* 3.1 34.0 + - + +
28A ARG* 1.3 94.0 + - - +
30A SER* 1.3 60.2 + - - +
32A LYS* 3.4 13.4 - - - +
33A GLN* 3.3 21.1 + - - +
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Residues in contact with SER 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 4.7 4.8 - - - +
25A LYS* 3.9 19.1 + - - +
26A PRO 3.6 1.5 + - - -
27A LEU* 2.9 28.1 + - - -
29A ASP* 1.3 77.8 - - - +
31A VAL* 1.3 61.5 + - - +
33A GLN* 3.5 8.1 + - - +
34A ALA* 3.1 22.5 + - - +
13B VAL* 4.0 16.6 - - - +
27B LEU* 3.9 3.4 - - - +
30B SER* 3.4 23.8 + - - -
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Residues in contact with VAL 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.0 25.3 + - + +
28A ARG* 3.6 9.4 - - - +
30A SER* 1.3 73.0 - - - +
32A LYS* 1.3 68.0 + - - +
34A ALA* 3.2 7.9 + - - +
35A LEU* 3.1 34.7 + - + +
54A VAL* 5.2 5.6 - - + -
58A VAL* 5.8 0.2 - - + -
27B LEU* 4.2 24.5 - - + -
31B VAL* 5.9 1.1 - - + -
58B VAL* 4.2 38.6 - - + +
61B PRO* 3.8 18.4 - - + -
62B LEU* 4.8 0.9 - - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ARG* 3.0 18.5 + - + +
29A ASP* 3.4 17.7 - - - +
31A VAL* 1.3 77.6 - - - +
33A GLN* 1.3 57.1 + - - +
35A LEU* 3.4 6.7 + - - +
36A LYS* 2.8 32.9 + - + +
61B PRO* 3.9 21.8 - - + +
64B ASP* 3.5 23.5 + - - +
65B MET* 3.5 28.3 - - - +
68B GLN* 3.7 17.0 + - - -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.7 10.7 + - - -
29A ASP 3.3 10.3 + - - +
30A SER* 3.7 6.6 - - - +
31A VAL 3.2 0.2 - - - -
32A LYS* 1.3 76.2 - - - +
34A ALA* 1.3 67.1 + - - +
35A LEU 3.0 0.3 + - - -
36A LYS* 3.1 11.9 + - + +
37A ASN* 2.8 31.7 + - + +
12B THR 5.3 1.1 + - - +
13B VAL* 3.2 23.5 - - - +
14B SER* 3.5 37.0 + - - +
24B GLN* 5.0 0.4 + - - -
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER 3.1 12.3 + - - +
31A VAL 3.3 9.4 - - - +
33A GLN* 1.3 76.4 - - - +
35A LEU* 1.3 58.1 + - + +
37A ASN* 3.6 5.7 + - - +
38A TYR* 3.0 26.0 + - - +
11B LEU* 4.2 12.9 - - + +
12B THR 3.6 29.3 + - - +
13B VAL* 5.1 0.4 - - - +
27B LEU* 4.0 27.1 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.1 25.3 + - + +
32A LYS* 3.6 4.9 - - - +
33A GLN 3.1 0.4 - - - -
34A ALA* 1.3 77.0 - - + +
36A LYS* 1.3 69.2 + - - +
37A ASN 2.9 1.8 - - - -
38A TYR* 2.6 20.0 + - + -
39A PHE* 2.7 35.8 + - + -
50A LEU* 4.1 26.7 - - + -
54A VAL* 4.4 7.9 - - + -
11B LEU* 4.4 13.5 - - + -
61B PRO 4.4 1.1 - - - +
62B LEU* 3.7 42.0 - - + +
65B MET* 4.1 14.1 - - + -
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 2.8 23.1 + - + +
33A GLN* 3.4 12.6 - - + +
35A LEU* 1.3 72.8 - - - +
37A ASN* 1.3 59.7 + - - +
39A PHE* 3.7 10.2 + - - +
40A ALA* 3.3 18.9 + - - +
65B MET* 3.7 29.9 - - + +
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Residues in contact with ASN 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 2.8 23.4 + - + +
34A ALA 3.6 4.2 + - - +
35A LEU 2.8 2.2 + - - -
36A LYS* 1.3 69.9 - - - +
38A TYR* 1.3 70.4 + - - +
40A ALA* 2.8 16.6 + - - -
41A GLN* 2.8 50.3 + - - +
10B VAL 5.8 1.8 - - - -
11B LEU* 5.7 0.2 - - - +
12B THR* 3.5 34.3 + - - +
24B GLN* 3.8 10.2 - - - +
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Residues in contact with TYR 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A ALA 3.0 16.1 + - - +
35A LEU* 2.6 17.5 + - + +
37A ASN* 1.3 76.3 - - - +
39A PHE* 1.3 69.0 + + - +
41A GLN* 3.3 15.6 + - + +
42A LEU* 3.3 45.9 + - + +
47A VAL* 4.0 27.1 - - + +
50A LEU* 3.9 26.5 - - + -
53A LEU* 4.3 8.2 - - + +
10B VAL* 3.2 37.3 - - + +
11B LEU* 3.5 17.9 - - + -
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Residues in contact with PHE 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 2.7 52.0 + - + +
36A LYS* 3.7 9.0 - - - +
38A TYR* 1.3 77.1 - + - +
40A ALA* 1.3 54.6 + - - +
41A GLN 3.4 0.3 + - - -
42A LEU* 2.8 40.5 + - + +
47A VAL* 4.7 2.9 - - + -
50A LEU* 3.9 22.0 - - + -
65B MET* 4.3 20.0 - - + -
66B VAL* 4.0 17.0 - - + -
69B TYR* 3.7 40.6 - + + -
80B MET* 3.6 25.4 - - + -
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LYS 3.3 10.5 + - - +
37A ASN* 2.8 14.3 + - - +
39A PHE* 1.3 79.7 - - - +
41A GLN* 1.3 71.7 + - - +
42A LEU 3.5 1.4 + - - +
43A ASN* 3.5 12.5 - - - +
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ASN* 2.8 46.3 + - - +
38A TYR* 3.6 11.4 - - + +
39A PHE 3.2 0.8 - - - -
40A ALA* 1.3 86.3 - - - +
42A LEU* 1.3 62.1 + - + +
43A ASN* 3.4 9.9 + - - +
45A GLN* 4.6 3.3 + - - -
5B ARG* 5.7 9.0 - - - +
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Residues in contact with LEU 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR* 3.3 51.8 - - + +
39A PHE* 2.8 32.0 - - + +
40A ALA 3.4 2.5 - - - +
41A GLN* 1.3 78.4 - - + +
43A ASN* 1.3 60.4 + - - +
44A GLY 3.1 5.8 + - - -
45A GLN* 3.5 41.5 - - + +
47A VAL* 3.4 32.8 - - + -
69B TYR* 5.1 7.4 + - - +
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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