Contacts of the helix formed by residues 250 - 261 (chain A) in PDB entry 1BJW
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 LYS 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A THR* 3.5 11.2 + - - +
92A GLU* 3.3 40.2 + - + +
93A GLU* 3.5 37.3 + - - +
248A GLY 3.1 6.0 + - - -
249A PRO* 1.3 70.2 - - - +
251A GLU* 1.3 56.4 + - - +
253A ILE* 3.5 5.9 + - - +
254A LYS* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A TYR* 4.2 12.4 + - - -
249A PRO* 4.5 10.7 - - + +
250A LYS* 1.3 73.7 - - - +
252A VAL* 1.3 76.3 + - + +
254A LYS* 3.7 19.1 - - - +
255A ALA* 3.3 20.3 + - - +
2B ARG* 5.5 4.9 + - - +
3B GLY* 5.4 4.3 - - - -
4B LEU* 4.1 23.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.7 2.2 - - + -
110A ALA* 5.2 1.6 - - + -
111A ILE* 4.2 19.5 - - + -
199A TYR* 3.7 36.1 - - + +
227A LEU* 3.5 26.7 - - + -
249A PRO* 2.8 27.6 + - + +
251A GLU* 1.3 77.2 - - + +
253A ILE* 1.3 58.3 + - - +
255A ALA* 3.1 3.6 + - - +
256A MET* 2.9 40.4 + - + +
4B LEU* 4.3 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ALA* 5.7 0.2 - - + -
74A ARG* 4.2 5.4 - - - +
92A GLU 3.9 15.5 - - - +
93A GLU 3.4 18.6 - - - +
94A THR 3.8 21.8 - - - +
95A ILE* 4.0 22.0 - - + +
227A LEU* 4.9 5.2 - - + -
246A ALA* 4.5 1.6 - - + -
247A CYS* 4.0 23.1 - - - +
248A GLY* 3.6 17.7 - - - +
249A PRO 3.1 2.5 + - - +
250A LYS 3.8 6.7 - - - +
252A VAL* 1.3 76.5 - - - +
254A LYS* 1.3 56.9 + - - +
256A MET* 3.2 24.5 + - - +
257A ALA* 2.9 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LYS* 3.1 18.2 + - + +
251A GLU* 3.7 22.9 + - - +
253A ILE* 1.3 78.1 - - - +
255A ALA* 1.3 63.1 + - - +
257A ALA* 3.3 8.5 + - + +
258A SER* 3.1 25.6 + - - +
4B LEU* 4.9 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA* 3.9 12.6 - - + -
251A GLU 3.3 12.4 + - - +
252A VAL 3.1 9.3 + - - +
254A LYS* 1.3 79.2 - - - +
256A MET* 1.3 66.9 + - - +
258A SER* 3.1 16.8 + - - -
259A VAL* 3.2 17.5 + - - +
4B LEU* 4.0 19.5 - - + -
8B VAL* 3.7 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ILE* 3.9 27.6 - - + -
97A THR* 4.8 0.9 - - + -
103A ALA* 3.2 39.9 - - + +
106A ASN* 3.5 16.4 + - + +
107A LEU* 4.0 40.8 - - + +
110A ALA* 4.5 2.9 - - + -
227A LEU* 5.2 0.9 - - - -
229A VAL* 6.1 0.4 - - + -
246A ALA* 4.4 6.7 - - + -
252A VAL* 2.9 18.5 + - + +
253A ILE* 3.2 28.7 + - - +
255A ALA* 1.3 75.5 - - - +
257A ALA* 1.3 60.9 - - - +
259A VAL* 3.2 4.8 + - - +
260A SER* 3.2 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 3.8 8.2 - - + +
68A ALA* 4.1 28.9 - - + +
95A ILE* 3.7 8.5 - - + +
253A ILE* 2.9 13.7 + - + +
254A LYS* 3.6 13.0 - - + +
255A ALA 3.2 0.2 - - - -
256A MET* 1.3 75.8 - - - +
258A SER* 1.3 58.1 + - - +
260A SER* 3.4 6.7 + - - -
261A SER* 3.0 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A LYS* 3.1 17.1 + - - +
255A ALA* 3.1 13.8 + - - -
257A ALA* 1.3 76.0 - - - +
259A VAL* 1.3 63.1 + - - +
261A SER* 2.8 23.2 + - - -
262A GLN* 3.4 17.1 + - - +
8B VAL* 4.6 1.6 - - - -
11B MET* 3.7 25.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 5.1 1.3 - - + -
106A ASN* 3.5 44.4 - - - +
109A GLN* 4.4 8.3 - - + -
110A ALA* 4.6 1.6 - - + +
255A ALA 3.2 14.1 + - - +
256A MET 3.2 7.4 + - - +
258A SER* 1.3 74.6 - - - +
260A SER* 1.3 59.6 + - - +
262A GLN* 3.4 8.6 + - - +
263A SER* 2.6 34.4 + - - +
8B VAL* 4.2 11.7 - - + -
11B MET* 5.0 0.4 - - - -
105B PHE* 5.0 8.4 - - + -
134B PHE* 3.8 35.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO 3.9 19.2 + - - -
95A ILE* 4.5 6.6 - - - +
96A VAL 5.2 1.0 + - - -
97A THR* 4.8 2.8 - - - +
102A GLN* 4.2 7.8 + - - -
106A ASN* 2.9 24.0 + - - +
256A MET 3.2 8.4 + - - -
257A ALA* 3.6 9.4 - - - -
258A SER 3.3 0.2 - - - -
259A VAL* 1.3 77.3 - - - +
261A SER* 1.3 59.3 + - - +
263A SER* 3.0 6.4 + - - -
264A THR* 2.9 19.0 + - - -
265A THR 2.8 28.6 + - - -
266A SER* 5.6 0.9 - - - -
267A PRO* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PRO* 4.1 19.3 - - - +
257A ALA 3.0 12.1 + - - -
258A SER* 2.8 26.0 + - - -
260A SER* 1.3 78.1 - - - +
262A GLN* 1.3 60.5 + - - +
263A SER 3.4 0.2 - - - -
265A THR* 4.2 10.7 + - - +
101B LYS* 2.8 28.1 + - - -
127B SER* 4.6 1.6 + - - -
130B GLU* 5.5 0.2 - - - +
----------------------------------------------------------
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