Contacts of the helix formed by residues 27 - 42 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 5.2 0.7 - - + -
30A SER* 3.9 26.0 - - - +
31A VAL* 4.2 24.9 - - + +
34A ALA* 4.0 17.9 - - + -
54A VAL* 5.5 3.8 - - + -
57A GLU* 4.3 14.8 + - + -
58A VAL* 5.3 8.7 - - + -
8B SER 4.5 0.4 + - - -
11B LEU* 3.0 38.2 + - + +
13B VAL* 4.7 4.7 - - + -
26B PRO* 1.3 68.6 - - - +
28B ARG* 1.3 67.8 + - - +
29B ASP 3.0 2.2 - - - -
30B SER* 2.8 32.6 + - - +
31B VAL* 3.1 17.4 + - + +
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Residues in contact with ARG 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ALA* 5.6 0.8 - - - +
57A GLU* 3.2 51.7 + - + +
60A GLN* 3.3 29.7 + - - +
61A PRO* 3.5 25.6 - - + +
7B ASN* 4.2 10.5 - - - +
8B SER* 3.2 33.6 - - - +
26B PRO* 4.3 9.0 - - + -
27B LEU* 1.3 76.1 - - - +
29B ASP* 1.3 64.8 + - - +
31B VAL* 3.1 8.6 + - - +
32B LYS* 3.0 26.7 + - + +
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Residues in contact with ASP 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 3.9 22.5 + - + +
26B PRO* 3.5 31.6 + - - +
27B LEU 3.0 1.0 + - - -
28B ARG* 1.3 84.9 - - - +
30B SER* 1.3 64.0 + - - +
32B LYS* 3.6 20.5 - - + +
33B GLN* 3.1 24.3 + - - +
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Residues in contact with SER 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A VAL* 3.4 17.1 - - - +
27A LEU* 3.6 11.7 - - - -
30A SER* 3.4 18.0 + - - -
13B VAL* 3.3 29.3 - - - +
25B LYS* 3.4 14.3 + - - +
26B PRO 3.9 0.8 + - - -
27B LEU* 2.8 16.1 + - - -
29B ASP* 1.3 75.5 - - - +
31B VAL* 1.3 64.1 + - - -
33B GLN* 3.3 1.4 + - - -
34B ALA* 3.0 20.1 + - - +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.9 28.3 - - + -
31A VAL* 5.9 1.3 - - + -
57A GLU 4.5 3.1 - - - +
58A VAL* 4.1 42.8 - - + +
61A PRO* 3.8 14.1 - - + -
62A LEU* 4.4 0.9 - - + +
27B LEU* 3.1 18.1 + - + +
28B ARG 3.1 7.7 + - - +
30B SER* 1.3 77.8 - - - +
32B LYS* 1.3 62.7 + - - +
34B ALA* 3.4 2.1 + - - +
35B LEU* 3.2 39.8 + - + +
54B VAL* 5.2 3.6 - - + -
58B VAL* 5.5 0.4 - - + -
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Residues in contact with LYS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO* 3.9 20.0 - - + -
64A ASP* 3.2 37.7 + - - -
65A MET* 4.0 32.8 - - + +
68A GLN* 5.4 0.2 + - - -
28B ARG* 3.0 12.6 + - - +
29B ASP* 3.6 22.9 - - - +
31B VAL* 1.3 78.4 - - - +
33B GLN* 1.3 58.3 + - - +
35B LEU* 3.2 3.7 + - - +
36B LYS* 2.9 29.8 + - - +
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR 4.7 0.2 - - - -
13A VAL* 3.8 19.7 - - - +
14A SER* 3.5 39.1 + - - +
25B LYS* 3.3 25.7 - - - +
29B ASP 3.1 12.2 + - - +
30B SER* 3.8 2.0 - - - +
32B LYS* 1.3 79.4 - - - +
34B ALA* 1.3 63.5 + - - +
36B LYS* 3.6 20.6 - - + +
37B ASN* 3.2 26.4 + - + +
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Residues in contact with ALA 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.2 11.3 - - + +
12A THR 3.5 26.2 + - - +
13A VAL* 3.6 13.8 - - + +
27A LEU* 4.0 18.8 - - + -
30B SER 3.0 17.7 + - - +
31B VAL 3.8 5.2 - - - +
32B LYS 3.3 0.2 - - - -
33B GLN* 1.3 76.6 - - - +
35B LEU* 1.3 56.7 + - + +
37B ASN* 2.8 18.7 + - - -
38B TYR* 3.3 12.6 + - - +
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Residues in contact with LEU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.5 9.2 - - + -
62A LEU* 3.7 42.0 - - + +
65A MET* 4.1 15.0 - - + -
31B VAL* 3.2 36.6 + - + +
32B LYS 3.5 6.1 - - - +
33B GLN 3.1 0.2 - - - -
34B ALA* 1.3 76.0 - - + +
36B LYS* 1.3 59.8 + - - +
37B ASN 3.1 2.2 - - - -
38B TYR* 2.9 8.8 + - + +
39B PHE* 2.8 49.2 + - + -
50B LEU* 4.0 25.1 - - + -
54B VAL* 4.5 9.0 - - + -
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A MET* 4.8 10.5 - - - -
32B LYS 2.9 13.8 + - - +
33B GLN* 3.3 25.1 + - + +
35B LEU* 1.3 77.0 - - - +
37B ASN* 1.3 63.3 + - + +
39B PHE* 3.5 13.8 + - - +
40B ALA* 3.3 20.4 + - - +
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Residues in contact with ASN 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A VAL 4.5 2.2 + - - -
12A THR* 2.9 30.9 + - - +
14A SER* 5.8 2.7 - - - +
24A GLN* 3.9 15.0 + - - +
33B GLN* 3.2 12.4 + - + +
34B ALA 2.8 28.5 + - - -
35B LEU 3.1 0.2 - - - -
36B LYS* 1.3 78.0 - - + +
38B TYR* 1.3 69.3 + - - +
39B PHE 3.2 1.1 - - - -
40B ALA* 3.4 12.9 + - + +
41B GLN* 2.9 45.5 + - - +
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Residues in contact with TYR 38 (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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10A VAL* 3.9 40.6 - - + +
11A LEU* 4.5 4.7 - - + -
34B ALA 3.3 13.7 - - - +
35B LEU* 2.9 18.1 + - + +
37B ASN* 1.3 85.2 - - - +
39B PHE* 1.3 76.9 + + - +
41B GLN* 3.6 9.2 + - + +
42B LEU* 3.5 30.9 + - + +
47B VAL* 3.3 34.0 - - + +
50B LEU* 3.6 26.7 - - + -
53B LEU* 4.1 15.6 - - + +
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Residues in contact with PHE 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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65A MET* 4.2 20.2 - - + -
66A VAL* 4.1 23.1 - - + -
69A TYR* 4.0 36.8 - + + -
80A MET* 3.4 30.3 - - + -
35B LEU* 2.8 41.2 + - + -
36B LYS* 3.6 12.3 - - - +
37B ASN 3.2 0.2 - - - -
38B TYR* 1.3 84.0 - + - +
40B ALA* 1.3 63.9 + - - +
41B GLN 3.1 1.6 - - - -
42B LEU* 2.4 31.3 - - + +
43B ASN* 4.1 4.9 - - - +
50B LEU* 4.2 11.7 - - + -
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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
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36B LYS 3.3 11.1 + - - +
37B ASN* 3.4 16.4 + - + +
39B PHE* 1.3 77.7 - - - +
41B GLN* 1.3 72.3 + - - +
43B ASN* 3.8 12.6 - - - +
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Residues in contact with GLN 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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37B ASN* 2.9 35.6 + - - +
38B TYR* 3.7 11.8 - - + +
39B PHE 3.1 0.6 - - - -
40B ALA* 1.3 86.7 - - - +
42B LEU* 1.3 53.3 + - + +
43B ASN* 2.5 25.0 + - - +
45B GLN* 5.2 0.2 - - - +
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Residues in contact with LEU 42 (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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69A TYR* 4.6 14.3 + - + +
80A MET* 4.4 13.2 - - + -
38B TYR* 3.5 24.2 + - + +
39B PHE* 2.4 47.3 - - + +
41B GLN* 1.3 70.4 - - + +
43B ASN* 1.3 61.0 + - - +
44B GLY* 3.3 13.5 - - - -
45B GLN* 3.1 35.0 - - - +
47B VAL* 3.4 32.8 - - + -
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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
------------------------------------------------------------
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