Contacts of the helix formed by residues 35 - 48 (chain A) in PDB entry 1BRW
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 ASP 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR* 3.3 28.1 + - - -
33A ILE 3.9 0.4 + - - +
34A PRO* 1.3 73.2 - - - +
36A TYR* 1.3 53.7 + - - +
38A MET* 3.0 9.0 + - - +
39A SER* 2.8 36.4 + - - -
163A LYS* 5.2 6.5 - - - -
167A LEU* 3.5 22.2 - - + +
1036B TYR* 3.8 20.7 - - + -
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Residues in contact with TYR 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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34A PRO* 3.6 27.1 - - + +
35A ASP* 1.3 77.9 - - - +
37A GLN* 1.3 79.6 + - + +
39A SER* 3.2 10.4 + - - -
40A ALA* 3.7 5.9 + - - +
1035B ASP* 3.8 38.4 - - + +
1036B TYR* 3.8 4.1 - - - +
1039B SER* 2.9 24.0 + - - +
1167B LEU* 3.8 7.4 - - + -
1170B VAL* 3.8 18.2 - - + -
1171B THR* 3.8 12.2 - - + +
1367B LYS* 4.0 5.9 - - - +
1368B LYS* 3.1 48.9 + - + +
1369B GLU 5.1 0.2 + - - -
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Residues in contact with GLN 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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3A MET* 3.7 36.1 - - + +
4A VAL* 3.3 10.1 - - - +
7A ILE* 3.6 17.6 - - + +
32A ASP 5.1 0.3 - - - +
33A ILE* 4.1 4.3 - - + +
34A PRO* 3.2 32.4 + - + +
35A ASP 3.1 0.6 - - - -
36A TYR* 1.3 91.4 - - + +
38A MET* 1.3 64.2 + - - +
39A SER 3.4 0.2 - - - -
40A ALA* 3.6 1.0 + - - -
41A LEU 3.2 17.0 + - - -
1170B VAL* 3.1 30.3 + - - +
1171B THR* 4.5 0.4 - - + -
1366B ALA 3.1 23.8 + - - -
1367B LYS* 4.6 7.1 - - - +
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Residues in contact with MET 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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3A MET* 4.2 11.1 - - - +
24A ILE* 4.0 29.6 - - + -
25A VAL* 5.5 7.6 - - + -
28A TYR* 3.9 39.9 - - + -
33A ILE* 4.9 2.2 - - + -
34A PRO 3.3 8.7 + - - +
35A ASP 3.0 7.0 + - - +
37A GLN* 1.3 77.8 - - - +
39A SER* 1.3 60.6 + - - +
41A LEU* 3.4 10.7 + - + +
42A ALA* 2.9 28.8 + - - +
58A LEU* 6.0 3.4 - - + -
164A LEU* 3.9 29.2 - - + -
167A LEU* 3.6 20.9 - - + -
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Residues in contact with SER 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 ASP 2.8 17.9 + - - -
36A TYR* 3.2 3.5 + - - -
38A MET* 1.3 75.1 - - - +
40A ALA* 1.3 63.0 + - - +
42A ALA* 3.3 7.0 + - - +
43A MET* 3.0 24.1 + - - +
167A LEU* 3.9 8.9 - - - +
171A THR* 3.8 21.8 + - - -
173A THR* 5.0 1.4 - - - +
1036B TYR* 2.9 21.8 + - - -
1039B SER* 2.8 26.2 + - - -
1040B ALA* 4.5 6.0 - - - +
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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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7A ILE* 4.4 4.3 - - + -
36A TYR 3.7 13.9 + - - +
37A GLN 3.6 5.8 + - - +
38A MET 3.3 0.4 - - - -
39A SER* 1.3 83.2 + - - +
41A LEU* 1.3 61.6 + - - +
43A MET* 3.2 6.4 + - - +
44A ALA* 3.0 21.7 + - - +
1039B SER* 4.4 17.3 - - - +
1043B MET* 3.9 14.7 - - + +
1171B THR* 4.0 29.6 - - - +
1173B THR* 5.1 0.2 - - + -
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Residues in contact with LEU 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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3A MET* 4.0 21.1 - - + -
6A LEU* 4.7 1.1 - - + +
7A ILE* 4.2 19.2 - - + +
10A LYS* 4.0 28.7 - - + -
16A LEU* 4.6 12.1 - - + -
24A ILE* 4.1 27.4 - - + -
37A GLN 3.2 14.3 + - - +
38A MET* 3.7 14.8 - - + +
40A ALA* 1.3 78.2 - - - +
42A ALA* 1.3 57.5 + - - +
44A ALA* 3.1 6.7 + - - +
45A ILE* 2.9 44.5 + - + +
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Residues in contact with ALA 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 MET* 2.9 18.8 + - + +
39A SER* 3.5 9.2 - - - +
41A LEU* 1.3 77.6 - - - +
43A MET* 1.3 56.6 + - - +
45A ILE* 3.4 13.1 + - - +
46A TYR* 3.0 24.9 + - - +
164A LEU* 5.2 8.5 - - + -
167A LEU* 5.6 2.2 - - + -
168A ARG* 5.0 5.2 - - + -
171A THR* 5.2 0.4 - - - +
173A THR* 3.8 24.7 - - - +
179A LEU* 4.4 13.7 - - + +
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Residues in contact with MET 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 SER 3.0 13.1 + - - +
40A ALA 3.2 6.7 + - - +
42A ALA* 1.3 73.8 - - - +
44A ALA* 1.3 65.3 + - - +
46A TYR* 3.1 17.3 + - - +
47A PHE* 3.2 37.0 + - + -
171A THR 3.4 24.9 - - - +
173A THR* 3.6 16.7 - - + +
1007B ILE* 3.7 20.9 - - + -
1011B ARG* 4.2 19.1 - - + -
1040B ALA* 3.7 22.9 - - + +
1043B MET* 3.8 19.7 - - + -
1044B ALA* 3.9 11.2 - - + +
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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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7A ILE* 4.6 3.1 - - + +
10A LYS* 3.9 18.6 - - + -
11A ARG* 4.3 17.3 - - - +
40A ALA 3.0 13.0 + - - +
41A LEU* 3.1 12.1 + - - +
43A MET* 1.3 76.8 - - - +
45A ILE* 1.3 50.6 + - - +
47A PHE* 3.3 1.7 + - - +
48A ARG* 2.8 39.2 + - - +
1043B MET* 3.9 13.1 - - + +
1047B PHE* 4.3 11.0 - - - -
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Residues in contact with ILE 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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10A LYS* 4.0 19.1 - - + -
16A LEU* 6.0 0.2 - - + -
41A LEU* 2.9 40.2 + - + +
42A ALA* 3.7 9.6 - - - +
44A ALA* 1.3 72.1 - - - +
46A TYR* 1.3 64.2 + - - +
47A PHE 3.1 1.8 - - - -
49A GLY* 2.8 30.0 + - - +
50A MET* 4.2 26.9 - - + -
58A LEU* 5.4 2.2 - - + -
176A SER* 3.8 18.1 + - - +
178A PRO* 4.1 22.2 - - + -
179A LEU* 4.2 21.8 - - + -
6002A MES 4.4 1.0 + - - -
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Residues in contact with TYR 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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42A ALA 3.0 14.0 + - - +
43A MET* 3.3 17.0 - - - +
45A ILE* 1.3 77.7 - - - +
47A PHE* 1.3 77.3 + + - +
172A ALA 4.4 9.2 - - - -
173A THR* 4.3 8.1 - - + -
175A ASN* 3.4 37.3 - - + +
176A SER* 4.2 14.8 - - - -
6002A MES 3.3 53.0 + - - +
1011B ARG* 3.3 48.5 + - + -
1012B ASP* 4.2 6.2 + - - -
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Residues in contact with PHE 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 MET* 3.2 43.0 + - + -
44A ALA 4.0 3.8 - - - +
45A ILE 3.1 0.2 - - - -
46A TYR* 1.3 85.5 - + - +
48A ARG* 1.3 66.8 + - - +
49A GLY 3.7 0.2 - - - -
6002A MES 3.7 41.2 + - - +
1011B ARG* 3.5 35.9 - - + -
1044B ALA* 4.0 15.3 - - - -
1047B PHE* 3.5 44.6 - + + -
1048B ARG* 4.0 29.2 - - + -
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Residues in contact with ARG 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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10A LYS* 3.1 33.4 - - + +
11A ARG 3.0 20.0 + - - +
12A ASP* 4.8 6.0 - - - +
13A GLY* 3.7 18.5 - - - +
44A ALA 2.8 20.6 + - - +
47A PHE* 1.3 77.4 + - - +
49A GLY* 1.3 62.0 + - - +
6002A MES 2.9 13.6 + - - -
1046B TYR* 5.4 5.5 + - - -
1047B PHE* 3.6 27.2 - - + -
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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