Contacts of the helix formed by residues 39 - 52 (chain A) in PDB entry 2RPQ
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ILE* 3.8 4.8 - - - +
37A HIS* 3.5 6.7 - - + +
38A THR* 1.3 95.8 - - + +
40A LEU* 1.3 65.3 + - - +
41A SER* 3.5 14.6 - - - +
42A LYS* 3.2 18.5 + - - +
69A GLU 3.4 18.4 - - - +
70A THR* 4.9 3.8 - - - +
71A ASP 3.6 8.1 - - - +
72A THR* 4.1 7.4 - - + -
971B MET* 3.9 26.9 - - + -
972B ASP* 6.0 0.2 - - - +
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Residues in contact with LEU 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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38A THR 3.8 0.6 + - - -
39A PRO* 1.3 68.7 - - - +
41A SER* 1.3 65.1 + - - +
42A LYS 3.1 0.9 + - - -
43A LEU* 3.2 25.8 - - + +
44A MET* 3.1 34.0 + - + +
60A PHE* 3.9 24.5 - - + -
67A ILE* 4.0 28.5 - - + +
68A ASN 3.2 33.4 - - - +
69A GLU* 4.1 1.3 - - - -
71A ASP* 3.0 31.6 + - + +
72A THR* 4.1 3.0 - - - +
73A PRO* 5.2 1.1 - - + -
76A LEU* 5.4 0.7 - - + -
78A MET* 4.4 15.3 - - + -
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Residues in contact with SER 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A PRO* 3.5 21.3 - - - +
40A LEU* 1.3 78.2 - - - +
42A LYS* 1.3 58.0 + - - +
44A MET* 3.6 8.6 - - - +
45A LYS* 3.0 32.4 + - - +
69A GLU* 3.6 36.8 + - - -
971B MET* 5.1 2.1 - - - +
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Residues in contact with LYS 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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34A ILE* 4.8 1.3 - - + -
38A THR* 3.9 6.1 - - + -
39A PRO 3.2 12.5 + - - +
40A LEU 3.1 1.8 + - - -
41A SER* 1.3 79.4 + - - +
43A LEU* 1.3 62.3 + - - +
45A LYS* 3.5 25.3 + - - +
46A ALA* 3.1 25.4 + - - +
49A GLU* 5.2 7.3 + - - -
969B LEU* 3.9 30.7 - - + -
970B THR 3.7 23.9 + - - +
971B MET* 3.7 36.1 - - + +
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Residues in contact with LEU 43 (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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20A LEU* 3.4 29.2 - - + -
22A VAL* 3.4 34.1 - - + -
32A PHE* 3.0 45.8 - - + -
34A ILE* 3.6 23.6 - - + +
40A LEU* 3.2 35.4 + - + +
42A LYS* 1.3 78.4 - - - +
44A MET* 1.3 55.3 + - - +
46A ALA* 3.3 3.1 + - - +
47A TYR* 2.8 25.3 + - - +
60A PHE* 3.8 12.6 - - + -
73A PRO* 5.4 0.7 - - + -
78A MET* 5.3 1.1 - - + -
84A ILE* 5.8 0.2 - - + -
969B LEU* 4.7 3.4 - - + -
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Residues in contact with MET 44 (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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40A LEU* 3.1 25.6 + - + +
41A SER* 3.6 10.1 - - - +
42A LYS 3.3 0.2 - - - -
43A LEU* 1.3 76.9 - - - +
45A LYS* 1.3 61.0 + - - +
47A TYR* 3.3 5.1 - - - +
48A CYS* 3.2 26.5 + - - -
55A MET* 4.2 14.8 - - + +
58A ILE* 4.4 13.5 - - + +
59A ARG* 3.7 31.6 - - - +
60A PHE* 3.7 57.2 - - + +
67A ILE 5.7 1.6 - - - +
68A ASN 6.1 0.2 - - - -
69A GLU* 4.1 20.0 - - + +
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Residues in contact with LYS 45 (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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41A SER* 3.0 17.8 + - - +
42A LYS* 4.0 23.1 - - - +
44A MET* 1.3 74.7 - - - +
46A ALA* 1.3 61.0 + - - +
48A CYS* 3.2 14.3 + - + +
49A GLU* 3.1 35.2 + - + +
55A MET* 4.3 28.1 - - + +
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Residues in contact with ALA 46 (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 PHE* 4.1 2.5 - - + -
42A LYS* 3.1 20.3 + - - +
43A LEU* 3.4 9.9 - - - +
45A LYS* 1.3 76.1 - - - +
47A TYR* 1.3 61.0 + - - +
49A GLU* 3.3 12.3 + - - +
50A ARG* 3.0 50.1 + - - +
967B ILE* 4.0 21.3 - - + -
969B LEU* 5.2 2.7 - - + -
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Residues in contact with TYR 47 (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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22A VAL* 3.4 26.4 - - + +
24A GLY* 3.9 22.7 + - - -
28A SER* 3.9 12.4 + - - -
29A VAL 5.2 0.4 - - - -
30A VAL* 3.4 26.5 - - + -
32A PHE* 3.7 12.1 - + + -
43A LEU 2.8 15.8 + - - +
44A MET* 3.3 10.1 - - - +
46A ALA* 1.3 70.7 - - - +
48A CYS* 1.3 56.7 + - - +
51A GLN* 2.8 49.4 + - + +
52A GLY 3.9 0.3 + - - -
53A LEU* 3.3 26.1 - - + +
58A ILE* 3.7 23.6 - - + -
60A PHE* 3.8 13.2 - + - -
86A VAL* 3.9 12.1 - - + +
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Residues in contact with CYS 48 (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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44A MET 3.2 16.2 - - - -
45A LYS* 3.2 11.8 + - + +
47A TYR* 1.3 78.1 - - - +
49A GLU* 1.3 61.6 + - + +
52A GLY* 3.2 17.8 + - - -
53A LEU* 3.2 27.9 + - - +
54A SER 4.0 2.0 - - - -
55A MET* 3.6 40.8 - - + +
58A ILE* 4.0 13.5 - - - -
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Residues in contact with GLU 49 (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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42A LYS* 5.2 6.9 + - - -
45A LYS* 3.1 23.8 + - + +
46A ALA* 3.3 8.0 + - - +
48A CYS* 1.3 78.4 - - + +
50A ARG* 1.3 97.8 + - - +
52A GLY* 4.5 2.1 + - - -
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Residues in contact with ARG 50 (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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30A VAL* 4.7 3.8 - - + -
46A ALA* 3.0 38.8 + - - +
47A TYR 4.3 1.1 - - - +
49A GLU* 1.3 108.9 + - - +
51A GLN* 1.3 74.9 + - + +
52A GLY 3.6 0.8 + - - -
966B VAL* 4.5 9.9 + - + +
967B ILE* 3.5 41.8 - - + +
968B ASP 4.9 7.7 + - - +
969B LEU* 5.9 1.4 - - - +
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Residues in contact with GLN 51 (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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28A SER* 5.0 15.3 - - - -
29A VAL 5.1 6.5 - - - +
30A VAL* 3.8 35.7 - - + +
47A TYR* 2.8 34.4 + - + +
50A ARG* 1.3 81.2 - - + +
52A GLY* 1.3 61.0 + - - +
53A LEU* 3.6 14.8 - - + +
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Residues in contact with GLY 52 (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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47A TYR 3.9 0.2 + - - -
48A CYS 3.2 11.0 + - - -
49A GLU 4.5 1.5 + - - -
50A ARG 3.6 2.2 + - - -
51A GLN* 1.3 78.5 - - - +
53A LEU* 1.3 63.4 + - - +
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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