Contacts of the helix formed by residues 99 - 111 (chain B) 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 GLY 99 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 2.8 26.0 + - - -
98B VAL* 1.3 74.7 - - - +
100B GLY* 1.3 65.8 + - - -
101B LYS 3.0 3.4 - - - -
102B GLN 3.2 4.2 + - - -
234B LLP 3.5 16.2 - - - -
242B ARG* 3.3 18.9 + - - -
243B ILE 3.8 4.3 - - - -
244B GLY* 3.4 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B GLY* 1.3 73.7 - - - -
101B LYS* 1.3 60.4 + - - +
103B ALA* 3.2 7.4 + - - +
104B LEU* 3.1 26.9 + - - +
229B VAL* 3.8 9.1 - - - +
230B ASN 3.8 20.8 + - - -
234B LLP 2.7 27.5 + - - -
244B GLY* 3.5 5.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A SER 2.8 29.4 + - - +
262A GLN 3.6 19.5 - - - +
263A SER 3.5 10.8 - - - +
265A THR* 2.9 31.1 + - - +
99B GLY 3.0 1.0 - - - -
100B GLY* 1.3 76.8 - - - +
102B GLN* 1.3 56.3 + - - +
104B LEU* 3.2 12.3 + - - +
105B PHE* 2.9 26.0 + - - +
125B TRP* 3.7 25.1 - - + -
127B SER* 3.6 20.5 + - - +
131B MET* 4.4 7.0 - - - -
234B LLP 3.1 18.3 + - - +
242B ARG* 4.5 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A SER* 2.9 18.4 + - - +
264A THR* 4.3 5.3 - - + +
97B THR* 3.6 8.1 - - - -
98B VAL* 2.8 56.9 + - + +
99B GLY 3.2 2.4 + - - -
101B LYS* 1.3 73.6 - - - +
103B ALA* 1.3 60.1 + - - +
105B PHE* 4.2 4.7 - - + -
106B ASN* 2.8 57.0 + - - +
260B SER* 4.1 4.0 + - - -
263B SER* 3.8 7.9 + - - -
264B THR* 2.9 37.5 + - - +
267B PRO* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 3.4 30.4 + - + +
99B GLY 3.6 3.0 + - - -
100B GLY* 3.2 11.8 + - - +
102B GLN* 1.3 76.7 - - - +
104B LEU* 1.3 59.3 + - - +
106B ASN* 4.7 0.2 - - - -
107B LEU* 3.0 32.0 + - - +
229B VAL* 4.0 17.0 - - + -
245B TYR 4.8 2.2 - - - +
246B ALA* 4.3 18.2 - - + -
256B MET* 3.3 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLY 3.1 17.3 + - - +
101B LYS* 3.2 7.2 + - - +
103B ALA* 1.3 75.4 - - - +
105B PHE* 1.3 64.1 + - - +
107B LEU* 3.3 7.6 + - + +
108B PHE* 3.1 41.1 + - + -
125B TRP* 3.8 29.6 - - + -
128B TYR* 3.9 14.1 - - + -
131B MET* 3.8 13.2 - - + -
169B VAL* 5.3 0.4 - - + -
201B VAL* 3.8 29.2 - - + -
203B ASP* 3.8 19.5 - - + +
229B VAL* 4.0 17.3 - - + -
234B LLP 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A PHE* 4.3 27.8 - + - -
109A GLN* 5.4 0.2 - - - -
259A VAL* 5.0 5.6 - - + -
262A GLN* 3.5 27.4 - - + +
263A SER* 3.5 25.6 - - - -
101B LYS 2.9 16.6 + - - +
102B GLN* 3.4 5.8 + - + +
104B LEU* 1.3 77.7 - - - +
106B ASN* 1.3 77.7 + - - +
108B PHE* 3.4 4.3 + - - +
109B GLN* 3.1 56.7 + - + +
131B MET* 3.8 16.5 - - + -
134B PHE* 3.9 30.5 - + + -
259B VAL* 5.0 2.5 - - + -
263B SER* 6.0 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B THR* 4.6 5.9 - - - +
102B GLN* 2.8 45.6 + - - +
103B ALA 4.0 3.1 - - - +
105B PHE* 1.3 84.1 - - - +
107B LEU* 1.3 62.2 + - - +
109B GLN* 3.4 2.5 + - - +
110B ALA* 3.0 25.5 + - - +
256B MET* 3.4 27.6 + - + +
259B VAL* 3.7 22.3 - - + +
260B SER* 2.8 32.9 + - - +
263B SER* 4.8 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ALA 3.0 18.1 + - - +
104B LEU* 3.3 9.9 - - + +
105B PHE 3.2 0.2 - - - -
106B ASN* 1.3 76.9 - - - +
108B PHE* 1.3 67.5 + - + +
110B ALA* 3.0 5.2 + - - +
111B ILE* 3.0 56.4 + - + +
201B VAL* 3.8 31.4 - - + -
227B LEU* 4.2 24.5 - - + -
229B VAL* 3.9 28.0 - - + -
252B VAL* 5.3 0.9 - - + -
256B MET* 3.9 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ARG* 4.0 0.2 + - - -
104B LEU* 3.1 38.4 + - + +
105B PHE* 3.9 3.6 - - - +
107B LEU* 1.3 92.9 - - + +
109B GLN* 1.3 57.7 + - + +
111B ILE* 4.2 4.5 - - + -
112B LEU* 2.9 59.5 + - + +
118B VAL* 4.5 9.4 - - + -
128B TYR* 4.9 4.0 - + + -
131B MET* 3.9 44.6 - - + +
132B VAL* 4.2 19.3 - - + -
135B ALA* 3.9 5.8 - - + +
167B ALA* 4.8 3.4 - - + -
169B VAL* 3.9 27.8 - - + -
201B VAL* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A SER* 2.8 23.6 + - - -
7A ARG* 2.8 34.9 + - - +
8A VAL* 4.8 0.3 - - - +
105A PHE* 5.7 0.2 - - - -
109A GLN* 4.7 8.2 + - - +
134A PHE* 3.4 34.5 - - + +
105B PHE* 3.1 47.0 + - + +
106B ASN 3.7 5.6 - - - +
108B PHE* 1.3 74.8 - - + +
110B ALA* 1.3 50.7 + - - +
131B MET 5.3 0.8 + - - -
134B PHE* 3.8 23.6 + - - +
135B ALA* 3.7 27.1 - - - +
259B VAL* 4.4 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.4 13.4 - - + +
5A SER* 2.9 21.8 + - - -
8A VAL* 4.1 11.5 - - + +
106B ASN 3.0 18.4 + - - +
107B LEU* 3.0 5.8 + - - +
109B GLN* 1.3 78.9 - - - +
111B ILE* 1.3 62.5 + - + +
252B VAL* 4.9 2.7 - - + +
255B ALA* 4.1 24.0 - - + -
256B MET* 4.4 12.3 - - + +
259B VAL* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY 3.7 12.0 - - - +
4A LEU* 4.6 3.4 - - + -
5A SER* 4.0 6.0 + - - +
107B LEU* 3.0 42.1 + - + +
108B PHE* 4.2 7.6 - - + -
110B ALA* 1.3 84.2 - - - +
112B LEU* 1.3 67.2 + - + +
116B ASP* 3.6 0.2 - - - +
166B LYS* 2.8 33.5 + - + +
167B ALA* 4.2 18.8 - - + -
199B TYR* 3.6 43.7 - - + +
227B LEU* 5.0 0.7 - - + -
252B VAL* 4.3 20.0 - - + -
----------------------------------------------------------
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