Contacts of the helix formed by residues 91 - 102 (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 THR 91 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.9 18.2 - - - +
89A ASP* 3.0 21.8 + - - -
90A THR* 1.3 74.6 - - - +
92A THR* 1.3 59.2 - - - +
94A VAL* 2.9 5.9 + - - +
95A LEU* 2.8 37.1 + - + +
199A ASP* 4.9 1.1 - - - +
201A LYS* 4.5 0.3 + - - -
243A LEU* 3.4 13.9 - - - +
268A LEU* 3.9 5.4 - - - +
271A LEU* 3.5 11.4 - - + +
272A CYS* 4.0 16.2 - - - -
275A LEU* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.0 17.3 + - + +
89A ASP 4.9 1.8 + - - -
90A THR 3.2 1.2 + - - -
91A THR* 1.3 77.1 - - - +
93A LEU* 1.3 63.2 + - - +
95A LEU* 4.4 6.7 - - - -
96A GLY* 3.0 25.4 + - - +
97A PRO* 3.9 1.9 - - - +
108A LYS* 3.4 26.9 - - + -
120A THR* 3.9 19.5 - - + -
150A ILE* 3.8 23.2 - - + +
2001A PO4 2.7 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.0 15.4 + - + +
92A THR* 1.3 77.2 - - + +
94A VAL* 1.3 58.1 + - - +
97A PRO* 3.5 19.6 - - - +
120A THR* 4.1 13.2 - - + +
123A LYS* 3.9 35.7 - - + -
124A LEU* 3.7 37.0 - - + +
150A ILE* 5.6 2.9 - - + -
252A GLU 4.0 20.6 - - - +
253A VAL* 4.1 17.5 - - + -
256A ALA* 3.7 11.6 - - + +
260A LEU* 4.1 3.1 - - - +
309A PHE* 3.8 20.7 - - + -
312A PHE* 5.8 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.6 5.8 + - + +
91A THR 2.9 7.0 + - - +
93A LEU* 1.3 78.5 - - - +
95A LEU* 1.3 66.0 + - - +
96A GLY 3.4 0.6 + - - -
97A PRO* 3.5 3.5 - - - +
98A LEU* 3.1 30.1 + - + +
256A ALA* 3.6 39.3 - - + +
259A THR* 4.0 21.8 - - + +
260A LEU* 3.6 22.4 - - + +
268A LEU* 4.6 8.1 - - + -
272A CYS* 3.6 25.4 - - + -
300A ILE* 6.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LYS* 3.6 34.5 - - + -
91A THR* 2.8 29.7 + - + +
92A THR* 4.2 2.5 - - - +
94A VAL* 1.3 72.9 - - - +
96A GLY* 1.3 67.5 + - - +
98A LEU* 3.6 6.4 - - + +
99A VAL* 3.1 27.6 + - + +
272A CYS* 3.4 31.4 - - - +
275A LEU* 4.0 11.7 - - + -
276A GLY* 3.4 23.1 - - - +
279A MET* 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 3.0 15.8 + - - +
95A LEU* 1.3 80.7 - - - +
97A PRO* 1.3 65.4 - - - +
99A VAL* 3.4 8.1 - - - +
100A ALA* 3.3 21.7 + - - +
106A VAL* 3.8 12.0 - - - +
148A ILE* 3.5 14.7 - - - +
150A ILE* 4.7 4.3 - - - -
279A MET* 6.0 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR 3.9 3.4 - - - +
93A LEU* 3.5 16.6 - - - +
94A VAL 3.5 5.4 - - - +
96A GLY* 1.3 87.6 - - - +
98A LEU* 1.3 60.0 + - - +
100A ALA* 3.6 3.1 + - + -
101A SER* 3.2 25.1 + - - -
148A ILE* 3.9 17.7 - - + -
150A ILE* 4.9 3.4 - - + -
260A LEU* 4.5 3.8 - - + -
305A ALA 4.4 4.8 - - - +
308A ALA* 3.7 9.9 - - + +
309A PHE* 3.6 50.0 - - + +
312A PHE* 4.1 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A VAL* 3.1 25.4 + - + +
95A LEU* 3.6 7.4 - - + +
96A GLY 3.2 0.2 - - - -
97A PRO* 1.3 78.5 - - - +
99A VAL* 1.3 59.5 + - + +
101A SER* 2.7 22.4 + - - -
102A VAL* 4.1 1.4 + - - +
260A LEU* 4.3 7.5 - - + +
272A CYS* 4.5 26.2 - - + +
273A LEU* 4.3 21.1 - - + -
296A LEU* 3.7 34.1 - - + +
299A ALA* 4.6 1.8 - - + -
300A ILE* 3.6 30.7 - - + -
305A ALA* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.1 20.1 + - + +
96A GLY* 3.4 7.2 - - - +
98A LEU* 1.3 74.7 - - + +
100A ALA* 1.3 64.0 + - - +
101A SER 3.2 0.9 - - - -
102A VAL* 3.4 8.2 - - - +
104A VAL* 3.1 38.8 + - + +
106A VAL* 3.5 19.7 - - + -
276A GLY* 3.7 36.1 - - - +
279A MET* 4.1 22.2 - - + -
280A VAL* 4.2 8.3 - - + -
296A LEU* 4.2 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLY 3.3 17.4 + - - +
97A PRO* 4.2 4.5 - - + +
98A LEU 3.3 0.2 - - - -
99A VAL* 1.3 73.5 - - - +
101A SER* 1.3 59.7 + - - +
102A VAL 3.1 5.4 - - - -
103A GLY* 3.3 12.4 + - - -
104A VAL 3.4 11.8 - - - +
106A VAL* 4.1 1.6 - - + -
146A ASN 4.8 7.3 - - - +
147A GLY* 3.6 26.3 - - - +
148A ILE* 3.9 17.9 - - + -
308A ALA* 5.1 4.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A PRO 3.2 15.5 + - - -
98A LEU 2.7 19.1 + - - -
100A ALA* 1.3 79.0 - - - +
102A VAL* 1.3 58.0 + - - +
103A GLY 3.4 0.4 - - - -
299A ALA* 3.5 19.2 - - - +
304A ALA* 3.7 34.2 - - - +
305A ALA* 4.0 6.4 - - - -
308A ALA* 3.8 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL 3.4 15.3 - - - +
101A SER* 1.3 83.4 - - - +
103A GLY* 1.3 57.4 + - - +
104A VAL* 4.3 3.4 - - + -
280A VAL* 4.0 29.6 - - + -
285A LYS* 4.6 12.0 - - - +
295A LEU* 4.1 31.4 - - + +
296A LEU* 4.1 10.8 - - + -
299A ALA* 3.8 25.4 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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