Contacts of the helix formed by residues 155 - 167 (chain D) in PDB entry 3BRW
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 ASN 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23D PHE* 3.2 28.8 - - - +
151D LYS* 4.9 1.8 + - - +
154D VAL* 1.3 80.1 - - - +
156D GLU* 1.3 62.8 + - - +
157D ILE 2.8 15.6 + - - -
158D PHE* 2.9 18.0 + - - +
159D TYR* 3.3 45.3 + - + -
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Residues in contact with GLU 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 4.2 2.3 - - - +
144D LEU* 4.3 13.6 - - + +
153D ASN* 3.5 34.6 + - - +
155D ASN* 1.3 83.6 + - - +
157D ILE* 1.3 64.4 + - - +
159D TYR* 4.0 16.6 - - + -
160D ASP* 3.2 25.2 + - + +
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Residues in contact with ILE 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 6.3 0.2 - - + -
19D LEU* 4.8 9.6 - - + -
79D ALA* 4.2 21.5 - - + -
81D VAL* 6.3 0.2 - - + -
112D ILE* 3.7 14.4 - - + +
114D VAL* 3.4 28.0 - - + -
144D LEU* 3.4 15.5 - - + -
146D SER* 3.3 24.5 - - - +
153D ASN 3.2 13.6 + - - +
154D VAL* 3.4 17.3 - - - +
155D ASN 2.8 1.0 + - - -
156D GLU* 1.3 79.1 - - - +
158D PHE* 1.3 86.2 + - + +
160D ASP 3.6 0.2 + - - -
161D LEU* 3.6 19.6 + - + +
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Residues in contact with PHE 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.0 20.1 - - + +
8D VAL* 5.0 11.7 - - + -
19D LEU* 4.0 18.8 - - + -
20D THR* 4.6 9.2 - - - -
23D PHE* 3.5 50.9 - + + -
53D LEU* 4.3 3.6 - - + -
55D ILE* 3.6 37.2 - - + -
79D ALA* 5.4 1.6 - - + -
154D VAL 3.4 23.8 - - - -
155D ASN 2.9 5.7 + - - +
157D ILE* 1.3 90.4 - - + +
159D TYR* 1.3 67.0 + - - +
160D ASP 3.3 0.2 - - - -
161D LEU* 3.2 8.8 + - + +
162D VAL* 3.1 26.7 + - - +
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Residues in contact with TYR 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PHE* 4.0 14.4 - + - -
44D VAL* 3.4 45.9 - - + +
45D GLU 4.6 4.0 + - - -
46D VAL* 3.4 25.0 - - + +
53D LEU* 5.3 2.7 - - + -
155D ASN* 3.3 46.2 + - + +
156D GLU* 4.3 13.9 - - + -
158D PHE* 1.3 78.5 - - - +
160D ASP* 1.3 56.8 + - - +
161D LEU 3.2 0.3 + - - -
162D VAL* 3.2 4.7 + - - +
163D ARG* 2.9 51.5 + - - +
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Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 4.2 8.2 - - + +
142D ALA* 3.4 28.8 - - - +
144D LEU* 5.5 4.9 - - + +
156D GLU* 3.2 22.5 + - + +
157D ILE 4.1 3.1 - - - +
159D TYR* 1.3 76.0 - - - +
161D LEU* 1.3 57.0 + - - +
163D ARG* 3.8 23.8 - - - +
164D GLN* 2.9 37.5 + - - +
167D ARG* 5.3 2.8 + - - -
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Residues in contact with LEU 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.8 36.1 - - + -
7D VAL 5.3 0.4 - - - +
77D GLY* 4.1 12.1 - - - +
78D PHE 3.8 19.1 - - - +
79D ALA* 4.2 12.6 - - + +
110D PRO* 3.8 16.4 - - + +
111D MET 4.1 1.6 - - - +
112D ILE* 3.7 33.4 - - + +
157D ILE 3.6 13.6 + - - +
158D PHE* 3.2 13.4 + - + +
159D TYR 3.1 0.6 - - - -
160D ASP* 1.3 77.5 - - - +
162D VAL* 1.3 60.3 + - - +
163D ARG 3.2 0.2 - - - -
164D GLN* 3.0 8.4 + - - +
165D ILE* 2.9 34.4 + - - +
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Residues in contact with VAL 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D TYR* 3.5 41.7 - - + +
6D LEU* 4.7 3.4 - - + -
46D VAL* 3.4 33.4 - - + -
51D CYS* 3.9 2.2 - - - -
53D LEU* 3.8 32.1 - - + -
158D PHE 3.1 14.7 + - - +
159D TYR* 3.5 8.1 - - - +
161D LEU* 1.3 76.9 - - - +
163D ARG* 1.3 56.0 + - - +
165D ILE* 3.0 2.3 + - - +
166D ASN* 2.8 34.5 + - - +
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Residues in contact with ARG 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D VAL* 4.3 10.0 - - + +
47D ASP* 2.8 42.2 + - - +
159D TYR* 2.9 39.8 + - - +
160D ASP* 3.8 27.6 - - - +
161D LEU 3.2 0.2 - - - -
162D VAL* 1.3 75.9 - - + +
164D GLN* 1.3 59.3 + - + +
166D ASN* 3.9 10.1 + - - +
167D ARG* 3.3 36.9 + - - +
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D VAL 4.6 0.2 - - - +
110D PRO* 3.2 20.3 - - + +
111D MET* 2.8 47.7 + - - +
112D ILE* 4.6 1.2 - - - +
142D ALA* 3.5 9.1 - - - +
160D ASP* 2.9 40.3 + - - +
161D LEU* 3.0 13.7 + - - +
163D ARG* 1.3 76.1 - - - +
165D ILE* 1.3 65.7 + - - +
166D ASN 3.3 0.4 - - - -
167D ARG* 3.5 37.8 + - - +
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Residues in contact with ILE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 3.5 26.6 + - - +
4D TYR* 3.5 29.4 - - + -
6D LEU* 3.8 24.7 - - + -
76D GLN* 3.7 35.2 - - + +
77D GLY* 4.2 2.7 - - - +
110D PRO* 3.9 20.2 - - + -
161D LEU 2.9 18.8 + - - +
162D VAL 3.0 5.4 + - - +
164D GLN* 1.3 74.7 - - - +
166D ASN* 1.3 64.5 + - - +
167D ARG* 3.3 8.4 - - - +
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Residues in contact with ASN 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 2.9 16.9 + - - +
4D TYR* 2.4 30.9 + - - -
46D VAL* 4.8 9.1 + - - +
47D ASP* 5.2 6.1 + - - -
49D GLN* 5.4 10.8 - - - +
51D CYS* 5.6 0.2 - - - -
162D VAL* 2.8 26.2 + - - +
163D ARG* 4.0 10.5 - - - +
164D GLN 3.3 0.2 - - - -
165D ILE* 1.3 74.9 - - - +
167D ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D ASP* 5.3 3.2 + - - -
163D ARG* 3.3 32.4 + - - +
164D GLN* 3.5 35.0 - - - +
165D ILE 3.3 13.5 - - - +
166D ASN* 1.3 79.3 - - - +
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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