Contacts of the helix formed by residues 31 - 44 (chain A) in PDB entry 3RGZ
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 SER 31 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A GLN* 1.3 79.0 - - - +
32A LEU* 1.3 63.7 + - - +
33A TYR* 3.6 7.1 + - - +
34A ARG* 3.2 23.0 + - - +
35A GLU* 3.2 21.2 + - - +
900A SO4 2.6 29.0 + - - -
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Residues in contact with LEU 32 (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 GLN 3.9 0.6 + - - -
31A SER* 1.3 71.6 - - - +
33A TYR* 1.3 59.5 + - - +
35A GLU* 4.0 15.7 - - - +
36A ILE* 2.9 42.4 + - + +
60A ASN* 5.2 8.5 - - - +
61A PRO* 3.9 29.6 - - + -
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Residues in contact with TYR 33 (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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31A SER* 3.1 9.6 - - - +
32A LEU* 1.3 79.6 - - - +
34A ARG* 1.3 63.9 + - + +
36A ILE* 3.1 5.7 - - - +
37A HIS* 2.7 68.6 + + + -
900A SO4 3.3 27.8 - - - +
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Residues in contact with ARG 34 (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 GLN* 6.1 0.9 - - - +
31A SER* 3.2 13.6 + - - +
33A TYR* 1.3 81.4 - - + +
35A GLU* 1.3 58.1 + - - +
37A HIS* 3.3 4.4 + - - +
38A GLN* 2.8 76.4 + - - +
97A SER* 5.4 3.0 + - - -
99A THR* 5.7 5.1 + - - -
900A SO4 2.9 41.3 + - - +
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Residues in contact with GLU 35 (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 GLN* 4.0 15.6 + - + +
31A SER 3.2 15.0 + - - +
32A LEU* 3.6 15.1 - - - +
34A ARG* 1.3 78.5 - - - +
36A ILE* 1.3 63.3 + - - +
38A GLN* 3.7 1.4 - - - +
39A LEU* 3.0 32.1 + - + +
60A ASN* 5.2 0.9 - - - +
61A PRO* 3.2 25.1 - - + +
62A CYS* 5.3 0.5 - - - -
72A ASP 4.6 8.3 - - - +
73A LYS* 4.1 3.0 - - - +
74A VAL* 3.1 48.4 + - + +
98A LEU* 3.9 18.8 - - + -
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Residues in contact with ILE 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 LEU* 2.9 40.7 + - + +
33A TYR* 3.1 16.6 - - - +
35A GLU* 1.3 77.7 - - - +
37A HIS* 1.3 71.1 + - + +
39A LEU* 4.7 1.1 - - + -
40A ILE* 3.0 48.8 + - + +
56A SER 3.8 16.2 - - - +
57A SER* 4.2 15.7 - - - +
59A LYS 3.9 9.2 - - - +
61A PRO* 4.1 12.1 - - + -
64A PHE* 3.8 18.2 - - + -
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Residues in contact with HIS 37 (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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33A TYR* 2.7 71.9 + + + +
34A ARG* 3.9 4.7 - - - +
36A ILE* 1.3 84.2 - - + +
38A GLN* 1.3 58.9 + - + +
40A ILE* 4.2 3.5 - - - +
41A SER* 2.9 32.4 + - - -
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Residues in contact with GLN 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 ARG* 2.8 55.9 + - - +
35A GLU 3.7 3.6 - - - +
37A HIS* 1.3 75.9 - - + +
39A LEU* 1.3 64.0 + - - +
41A SER* 2.9 20.2 + - - +
42A PHE* 3.2 6.2 + - - +
93A SER 4.1 2.4 - - - +
94A SER* 3.1 34.0 - - - +
95A LEU* 4.9 0.4 - - - +
97A SER* 2.7 39.2 + - - +
98A LEU* 3.1 30.1 - - + +
99A THR* 4.8 2.4 + - - +
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Residues in contact with LEU 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 GLU* 3.0 28.3 + - + +
36A ILE* 3.9 3.1 - - - +
38A GLN* 1.3 74.8 - - - +
40A ILE* 1.3 58.9 + - - +
42A PHE* 3.2 8.5 + - - +
43A LYS 3.1 21.1 + - - -
55A TRP* 3.5 35.5 - - + -
61A PRO* 3.6 34.5 - - + -
64A PHE* 4.1 17.3 - - + -
67A VAL* 5.0 3.1 - - + -
74A VAL* 4.4 6.3 - - + -
77A ILE* 3.8 18.6 - - + -
95A LEU* 4.2 6.5 - - + -
98A LEU* 3.8 23.6 - - + -
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Residues in contact with ILE 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 ILE* 3.0 34.7 + - + +
37A HIS* 4.2 3.6 - - - +
39A LEU* 1.3 73.2 - - - +
41A SER* 1.3 59.4 + - - +
43A LYS* 3.2 7.5 + - + +
44A ASP* 2.8 47.0 + - - +
55A TRP* 4.0 10.3 - - + +
56A SER* 3.5 39.9 - - - +
57A SER* 3.9 16.6 - - - +
64A PHE* 4.3 7.2 - - + -
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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
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37A HIS 2.9 17.7 + - - -
38A GLN* 2.9 19.4 + - - +
40A ILE* 1.3 77.8 - - - +
42A PHE* 1.3 59.8 + - - +
44A ASP* 3.7 8.9 + - - +
45A VAL* 3.6 25.6 + - - +
94A SER* 3.2 13.5 + - - -
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Residues in contact with PHE 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 GLN 3.2 2.6 + - - +
39A LEU 3.2 8.7 + - - +
40A ILE 3.1 0.2 - - - -
41A SER* 1.3 79.8 + - - +
43A LYS* 1.3 68.4 + - - +
45A VAL* 3.1 25.7 + - + +
46A LEU* 3.6 25.7 + - + +
52A LEU* 4.3 13.0 - - + -
55A TRP* 4.3 4.9 - + - -
79A LEU* 3.8 21.8 - - + -
84A LEU* 4.0 21.1 - - + -
86A VAL* 4.4 9.9 - - + -
90A ALA* 3.8 19.7 - - + -
91A VAL* 4.0 25.4 - - + -
94A SER* 3.6 16.6 - - - -
95A LEU* 3.8 31.4 - - + -
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Residues in contact with LYS 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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39A LEU 3.1 12.8 + - - +
40A ILE* 3.6 12.6 - - + +
42A PHE* 1.3 77.9 - - - +
44A ASP* 1.3 68.9 + - - +
45A VAL 3.1 1.6 + - - -
46A LEU* 3.1 28.7 + - + +
49A LYS 5.4 4.0 - - - -
51A LEU 4.1 8.7 - - - +
52A LEU* 3.1 28.8 + - + +
53A PRO* 3.8 11.9 + - - +
55A TRP* 2.5 57.5 + - + +
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Residues in contact with ASP 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 ILE* 2.8 38.1 + - - +
41A SER* 3.9 10.0 - - - +
42A PHE 3.2 0.4 - - - -
43A LYS* 1.3 82.3 - - - +
45A VAL* 1.3 61.9 + - + +
46A LEU 3.5 2.3 - - - +
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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