Contacts of the helix formed by residues 86 - 99 (chain A) in PDB entry 6B3I
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 HIS 86 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.4 8.7 - - - -
47A ASP* 6.2 0.2 - - - -
50A GLN* 3.5 41.9 + - + +
85A ASP* 1.3 73.9 - - - +
87A PRO* 1.3 70.5 - - + +
88A SER* 4.2 7.9 - - - +
89A GLU* 2.8 52.6 + - + +
90A TYR* 3.1 10.4 + - - +
130A ARG* 5.2 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A SER* 4.2 15.9 - - - +
85A ASP 3.6 4.9 - - - +
86A HIS* 1.3 87.4 - - + +
88A SER* 1.3 63.4 + - - +
90A TYR* 4.1 6.5 - - + +
91A ALA* 3.2 24.1 + - - +
116A ARG* 5.3 1.0 + - - -
124A ILE* 5.5 0.2 - - - +
273A VAL* 4.8 7.4 - - + +
274A THR* 4.1 34.6 - - + +
277A GLU* 5.9 2.2 - - - +
278A VAL* 6.3 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A HIS* 3.0 6.1 - - - +
87A PRO* 1.3 81.7 - - - +
89A GLU* 1.3 60.0 + - - +
91A ALA* 3.4 3.8 + - - +
92A ALA* 3.0 26.5 + - - +
120A GLU* 5.2 0.5 + - - -
123A ALA* 3.3 44.4 - - - +
124A ILE* 3.9 14.0 - - - +
127A ALA* 4.0 5.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLN* 5.5 0.7 + - - -
85A ASP* 4.3 16.8 - - + +
86A HIS* 2.8 47.4 + - + +
88A SER* 1.3 75.7 - - - +
90A TYR* 1.3 59.7 + - - +
92A ALA* 3.0 5.7 + - - +
93A ARG* 2.9 37.4 + - - +
127A ALA* 3.8 21.5 - - + -
130A ARG* 3.2 23.3 + - - +
131A LEU* 3.9 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 4.8 6.8 + - + +
82A ALA* 3.5 36.3 - - + +
85A ASP* 4.2 17.1 - - + +
86A HIS 3.1 12.7 + - - +
87A PRO* 4.4 5.4 - - + +
89A GLU* 1.3 76.7 - - - +
91A ALA* 1.3 61.9 + - - +
93A ARG* 3.3 15.8 + - + +
94A GLN* 2.7 57.5 + - + +
266A GLU* 4.8 1.4 + - - -
269A ILE* 3.5 21.2 - - - +
270A ARG* 3.8 23.1 + - - -
273A VAL* 3.9 13.2 - - + -
274A THR* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO 3.2 21.4 + - - +
88A SER 3.7 4.7 - - - +
89A GLU 3.2 0.2 - - - -
90A TYR* 1.3 76.0 - - - +
92A ALA* 1.3 63.2 + - - +
94A GLN* 3.4 8.1 + - - +
95A LEU* 3.1 29.2 + - - +
112A VAL* 4.4 8.4 - - + +
116A ARG* 4.1 14.8 - - - +
124A ILE* 3.8 23.8 - - + -
270A ARG* 5.9 1.3 - - + -
274A THR* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A SER 3.0 12.8 + - - +
89A GLU* 3.0 12.4 + - - +
91A ALA* 1.3 75.2 - - - +
93A ARG* 1.3 63.4 + - - +
95A LEU* 3.3 3.2 + - - +
96A GLN* 3.0 19.1 + - - +
124A ILE* 4.1 11.8 - - + +
127A ALA 4.4 1.1 - - - -
128A TYR* 3.6 51.6 - - + +
131A LEU* 4.7 1.3 - - + -
132A PHE* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 5.2 3.4 + - - -
85A ASP* 3.2 37.7 + - - -
89A GLU* 2.9 25.4 + - - +
90A TYR* 3.6 17.3 - - + +
92A ALA* 1.3 77.5 - - - +
94A GLN* 1.3 57.0 + - + +
96A GLN* 3.2 2.4 + - - +
97A LYS* 2.9 31.3 + - - +
131A LEU* 3.8 31.0 - - + +
132A PHE* 4.1 18.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 2.7 58.5 + - + +
91A ALA* 3.7 6.3 - - - +
92A ALA 3.3 0.2 - - - -
93A ARG* 1.3 75.1 - - - +
95A LEU* 1.3 62.9 + - + +
97A LYS* 4.0 10.2 - - - +
98A ALA* 3.2 25.8 + - - +
108A VAL* 3.8 11.4 - - + +
112A VAL* 5.6 0.9 - - + -
266A GLU* 3.4 23.3 + - - +
270A ARG* 3.4 49.2 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
91A ALA 3.1 16.1 + - - +
92A ALA* 3.6 7.2 - - - +
93A ARG 3.2 0.2 - - - -
94A GLN* 1.3 75.1 - - - +
96A GLN* 1.3 63.8 + - - +
98A ALA* 3.4 3.4 + - - +
99A MET* 3.1 31.7 + - + +
108A VAL* 3.9 22.2 - - + +
109A LEU* 3.7 30.3 - - + +
112A VAL* 4.1 22.0 - - + -
113A LEU* 4.9 5.4 - - + -
124A ILE* 3.9 14.6 - - + -
128A TYR* 4.5 0.2 - - + -
136A LEU* 3.9 41.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 3.0 10.2 + - - +
93A ARG 3.8 2.8 - - - +
95A LEU* 1.3 76.9 - - - +
97A LYS* 1.3 66.7 + - - +
99A MET* 3.6 17.8 - - - +
128A TYR* 3.5 25.3 - - + +
132A PHE* 3.6 51.3 - - + -
134A ARG* 3.6 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A LYS* 3.0 20.2 - - - +
93A ARG 2.9 17.2 + - - +
94A GLN* 4.0 12.1 - - - +
96A GLN* 1.3 85.5 + - - +
98A ALA* 1.3 61.1 + - - +
99A MET 3.4 0.9 + - - +
100A LYS* 3.4 27.7 + - - +
266A GLU* 2.9 33.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A GLN 3.2 18.6 + - - +
95A LEU* 3.8 2.9 - - - +
97A LYS* 1.3 75.4 - - - +
99A MET* 1.3 59.7 + - - +
100A LYS* 3.5 13.2 + - - +
104A THR* 5.0 2.1 + - - -
105A ASP 4.0 18.9 - - - +
106A GLU* 5.1 2.5 - - - +
108A VAL* 3.8 29.8 - - + +
109A LEU* 5.3 3.8 - - + +
143A ASP* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU 3.1 21.5 + - - +
96A GLN* 3.6 12.8 - - + +
97A LYS 3.2 2.1 - - - +
98A ALA* 1.3 74.4 - - - +
100A LYS* 1.3 63.1 + - - +
106A GLU* 5.4 0.9 - - - +
109A LEU* 4.5 17.0 - - + -
128A TYR* 3.2 32.1 - - + +
136A LEU* 4.4 6.7 - - + -
139A ASP* 3.6 31.0 - - + +
140A VAL* 4.4 14.1 - - - -
143A ASP* 3.3 32.8 - - + +
----------------------------------------------------------
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