Contacts of the helix formed by residues 33 - 43 (chain A) in PDB entry 1RA4
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 GLY 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A LYS* 1.3 74.7 - - - +
34A ALA* 1.3 65.5 + - - -
35A ASN 3.3 2.8 + - - -
36A GLU 3.4 0.4 + - - -
37A VAL* 3.0 23.2 + - - +
94A ALA* 4.5 5.0 - - - +
95A SER* 4.1 9.6 - - - -
96A SER* 2.9 23.1 + - - -
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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
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33A GLY* 1.3 72.5 - - - -
35A ASN* 1.3 56.7 + - - +
37A VAL* 4.5 1.6 - - - -
38A THR* 2.7 40.2 + - - +
60A VAL* 3.3 32.8 - - + +
61A VAL* 4.2 3.1 - - + -
63A HIS* 4.9 2.5 - - + -
64A LEU* 5.0 1.8 - - + -
95A SER* 3.5 14.6 + - - +
96A SER* 3.3 11.0 + - - +
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Residues in contact with ASN 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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33A GLY 3.3 1.0 - - - -
34A ALA* 1.3 80.2 - - - +
36A GLU* 1.3 70.4 + - + +
38A THR* 3.7 4.3 - - - -
39A LYS* 3.0 55.2 + - - +
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Residues in contact with GLU 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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31A LYS* 4.0 35.0 + - + +
32A LYS 3.7 20.6 + - - +
33A GLY 3.4 2.6 + - - -
35A ASN* 1.3 82.1 - - + +
37A VAL* 1.3 66.4 + - - +
39A LYS* 3.3 21.9 + - - +
40A ALA* 2.9 24.1 + - - +
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Residues in contact with VAL 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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31A LYS* 3.7 9.4 - - - +
33A GLY 3.0 21.8 + - - +
34A ALA 4.1 1.6 - - - +
36A GLU* 1.3 76.7 - - - +
38A THR* 1.3 59.0 + - - +
40A ALA* 3.2 7.5 + - - +
41A VAL* 2.9 30.4 + - + +
49A VAL* 3.9 35.4 - - + -
64A LEU* 4.1 18.6 - - + -
96A SER* 3.7 8.1 - - - +
97A VAL* 3.6 15.7 - - - +
98A ALA* 3.5 27.3 - - + +
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Residues in contact with THR 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 2.7 23.1 + - - -
35A ASN* 3.7 4.9 - - - -
37A VAL* 1.3 75.5 - - - +
39A LYS* 1.3 62.1 + - + +
41A VAL* 2.6 26.6 - - - +
42A GLU* 3.0 33.4 + - - +
63A HIS* 2.8 31.0 + - + +
64A LEU* 3.6 6.6 - - - +
67A LEU* 3.6 15.7 - - + -
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Residues in contact with LYS 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 ASN* 3.0 40.3 + - - +
36A GLU* 3.7 25.4 - - - +
37A VAL 3.3 0.4 - - - -
38A THR* 1.3 78.8 - - + +
40A ALA* 1.3 56.4 - - - +
42A GLU* 3.3 17.3 + - - +
43A ARG* 2.9 39.6 + - + +
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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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31A LYS* 4.0 20.0 - - + -
36A GLU 2.9 16.8 + - - +
37A VAL 3.5 5.4 - - - +
39A LYS* 1.3 73.5 - - - +
41A VAL* 1.3 64.4 + - - +
43A ARG* 3.6 0.8 + - - +
44A GLY 3.1 2.6 + - - -
45A ILE* 3.0 50.8 + - + +
46A ALA* 3.4 4.5 + - + -
98A ALA* 4.2 9.2 - - + -
100A ILE* 4.0 8.5 - - + -
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Residues in contact with VAL 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 VAL 2.9 14.4 + - - +
38A THR* 2.6 29.2 - - - +
40A ALA* 1.3 72.2 - - - +
42A GLU* 1.3 65.3 + - - +
43A ARG 3.1 0.2 - - - -
44A GLY* 3.0 12.6 + - - -
46A ALA* 4.4 5.6 - - + +
49A VAL* 5.1 2.5 - - + -
64A LEU* 4.6 4.5 - - + -
67A LEU* 3.1 52.7 - - + +
68A CYS* 4.0 15.3 - - - -
71A LYS* 3.4 13.2 - - + +
73A ILE* 3.7 22.7 - - + +
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Residues in contact with GLU 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 THR* 3.0 43.3 + - - +
39A LYS* 3.6 17.4 + - - +
41A VAL* 1.3 78.4 - - - +
43A ARG* 1.3 60.4 + - + +
44A GLY 3.5 0.3 + - - -
67A LEU* 4.2 18.8 - - + +
71A LYS* 3.7 23.5 + - - +
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Residues in contact with ARG 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 LYS* 2.9 23.8 + - + +
40A ALA* 3.8 5.6 - - - +
41A VAL 3.1 0.4 - - - -
42A GLU* 1.3 76.2 - - + +
44A GLY* 1.3 60.7 + - - +
45A ILE* 3.5 43.8 + - + +
71A LYS* 5.1 1.6 - - - -
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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