Contacts of the helix formed by residues 37 - 49 (chain A) in PDB entry 3RRA
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 ARG 37 (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 2.8 10.8 + - - -
35A GLU 3.6 1.2 + - - -
36A GLY* 1.3 83.8 + - - -
38A ALA* 1.3 63.9 - - - +
40A THR* 4.2 3.1 - - - +
41A VAL* 3.2 22.2 + - - +
78A ILE* 4.1 15.0 - - + -
44B ALA* 5.9 0.4 - - - +
47B GLU* 3.2 33.0 + - - +
48B LEU* 3.7 19.4 - - - +
51B TYR* 2.6 47.8 + - - -
67B MET 3.7 12.1 + - - -
68B TYR 5.9 0.4 - - - -
71B GLY* 3.8 14.1 + - - +
72B PHE* 3.5 47.3 - - + +
79B LEU* 4.2 15.2 - - + +
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Residues in contact with ALA 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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10A ARG* 4.5 19.5 - - + -
16A MET* 4.6 4.0 - - - +
34A ILE* 3.7 34.1 + - + +
36A GLY 3.5 2.3 - - - +
37A ARG* 1.3 76.6 - - - +
39A ARG* 1.3 60.6 + - + +
41A VAL* 3.6 2.1 + - - +
42A GLU* 3.0 30.1 + - - +
47B GLU* 3.3 5.6 + - - +
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Residues in contact with ARG 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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10A ARG* 5.1 22.0 - - - +
37A ARG 3.4 0.4 - - - -
38A ALA* 1.3 77.1 - - + +
40A THR* 1.3 59.5 + - - +
42A GLU* 3.5 11.6 + - - +
43A ALA* 3.0 28.2 + - - +
43B ALA* 3.9 10.7 - - + +
47B GLU* 3.4 27.6 + - + +
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Residues in contact with THR 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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37A ARG* 3.7 13.6 - - - +
39A ARG* 1.3 74.1 - - - +
41A VAL* 1.3 60.1 + - - +
43A ALA* 3.2 4.7 + - - +
44A ALA* 2.9 27.0 + - - +
78A ILE* 3.8 23.1 - - + -
40B THR* 3.5 24.5 - - + +
43B ALA* 3.6 9.5 + - - +
44B ALA* 3.4 30.2 + - + +
47B GLU* 2.6 24.1 + - - +
78B ILE* 4.0 4.5 - - + -
79B LEU* 5.1 1.3 - - + +
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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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16A MET* 3.9 11.9 - - + -
32A PRO* 4.0 6.1 - - + -
33A VAL 3.8 14.6 - - - +
34A ILE* 3.9 22.2 - - + -
37A ARG* 3.2 18.8 + - + +
38A ALA 3.9 3.6 - - - +
40A THR* 1.3 75.2 - - - +
42A GLU* 1.3 62.3 + - - +
44A ALA* 3.1 3.2 + - - +
45A VAL* 3.0 26.0 + - + +
78A ILE* 4.1 30.5 - - + +
81A SER* 3.8 19.1 - - - +
82A ALA* 4.7 7.0 - - + +
72B PHE* 4.9 3.6 - - + -
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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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8A THR* 2.8 39.8 + - - +
10A ARG* 2.8 46.7 + - - +
16A MET* 4.0 17.7 - - - +
38A ALA 3.0 18.4 + - - +
39A ARG* 3.7 9.6 + - - +
40A THR 3.3 0.2 - - - -
41A VAL* 1.3 76.5 - - - +
43A ALA* 1.3 60.9 + - - +
45A VAL* 3.4 3.4 + - - +
46A HIS* 3.2 35.5 + - + -
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Residues in contact with ALA 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 ARG 3.0 15.5 + - - +
40A THR 3.2 8.0 + - - +
42A GLU* 1.3 73.0 - - - +
44A ALA* 1.3 60.1 + - - +
46A HIS* 3.4 6.4 + - - +
47A GLU* 3.0 32.9 + - - +
39B ARG* 3.8 17.5 - - + +
40B THR* 3.8 7.0 - - - -
43B ALA* 3.8 19.5 - - + -
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Residues in contact with ALA 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 THR 2.9 12.9 + - - +
41A VAL 3.1 9.2 + - - +
43A ALA* 1.3 74.5 - - - +
45A VAL* 1.3 65.1 + - - +
47A GLU* 3.3 2.0 + - - +
48A LEU* 3.0 28.9 + - - +
78A ILE* 3.9 12.1 - - + -
79A LEU* 4.2 12.6 - - + -
82A ALA* 3.8 18.6 - - + -
40B THR* 3.5 22.7 - - + +
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Residues in contact with VAL 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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6A LEU* 3.9 22.2 - - + -
8A THR* 3.8 22.4 - - + -
16A MET* 4.0 14.8 - - + -
18A LEU* 3.9 24.5 - - + -
32A PRO* 4.5 0.9 - - + -
41A VAL 3.0 18.5 + - - +
42A GLU 3.6 8.1 - - - +
43A ALA 3.3 0.2 - - - -
44A ALA* 1.3 75.1 - - - +
46A HIS* 1.3 61.3 + - + +
48A LEU* 3.3 4.3 + - - +
49A SER* 3.0 25.8 + - - -
82A ALA* 3.8 23.1 - - + +
86A ILE* 4.2 8.4 - - + +
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Residues in contact with HIS 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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6A LEU* 3.5 28.8 + - + +
7A THR* 4.4 1.1 - - + -
8A THR* 2.8 38.2 + - + +
42A GLU* 3.2 30.4 + - + +
43A ALA* 3.4 6.3 + - - +
44A ALA 3.3 0.2 - - - -
45A VAL* 1.3 76.8 - - + +
47A GLU* 1.3 61.4 + - + +
49A SER* 2.6 24.3 + - - -
50A ASP* 3.5 9.5 - - - +
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Residues in contact with GLU 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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43A ALA 3.0 19.7 + - - +
44A ALA 3.3 4.7 + - - +
46A HIS* 1.3 75.7 - - - +
48A LEU* 1.3 63.1 + - - +
49A SER 3.2 0.6 + - - -
50A ASP* 3.5 23.2 + - - +
51A TYR* 4.7 4.7 + - - -
36B GLY 4.4 3.4 - - - +
37B ARG* 3.2 32.2 + - - +
38B ALA* 3.5 7.8 + - - +
39B ARG* 3.2 43.7 + - + +
40B THR* 2.5 29.2 + - - +
369B ASN* 4.2 12.2 + - - +
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Residues in contact with LEU 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 ALA 3.0 21.4 + - - +
45A VAL 3.7 4.5 - - - +
47A GLU* 1.3 73.9 - - + +
49A SER* 1.3 63.8 + - - +
50A ASP 3.1 2.0 - - - -
51A TYR* 3.2 30.2 + - + +
52A LEU* 3.4 14.9 - - - +
67A MET* 3.9 19.7 - - + +
79A LEU* 4.5 12.6 - - + +
82A ALA* 3.8 19.7 - - + -
83A ILE* 3.8 26.0 - - + -
86A ILE* 4.0 14.6 - - + -
37B ARG* 3.6 34.8 - - - +
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Residues in contact with SER 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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6A LEU* 3.8 31.9 - - - -
45A VAL 3.0 12.3 + - - -
46A HIS* 2.6 31.3 + - - +
48A LEU* 1.3 74.9 - - - +
50A ASP* 1.3 60.2 + - - +
51A TYR 3.1 0.9 - - - -
52A LEU* 2.9 25.1 + - - -
53A ILE* 3.0 26.7 + - - +
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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