Contacts of the helix formed by residues 76 - 91 (chain A) in PDB entry 4QYJ
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 SER 76 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PRO* 3.2 5.6 + - - +
75A PRO* 1.3 77.9 - - - +
77A ALA* 1.3 60.6 + - - +
78A ARG 3.4 0.9 - - - -
79A GLU* 3.6 26.3 - - - +
80A ARG* 3.3 22.5 + - - +
131A THR* 4.7 4.5 - - - -
121C GLN* 4.3 29.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 3.7 20.3 - - + +
74A PRO* 3.3 25.4 - - + +
76A SER* 1.3 82.8 + - - +
78A ARG* 1.3 56.8 + - - +
79A GLU 3.3 0.4 - - - -
80A ARG* 3.5 6.5 + - - +
81A ILE* 3.2 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 3.0 64.3 + - + +
71A ARG* 4.1 9.3 + - - +
73A MET* 3.4 33.9 + - - +
74A PRO 3.7 4.4 + - - +
75A PRO* 4.4 12.5 - - + +
77A ALA* 1.3 77.6 - - - +
79A GLU* 1.3 60.8 + - - +
80A ARG 3.3 0.4 - - - -
81A ILE* 3.9 8.0 + - + +
82A LEU* 3.4 24.6 + - + +
130A ALA* 4.5 5.4 - - + +
183A LEU* 3.2 28.9 - - + +
184A ALA* 4.0 12.0 + - - +
185A CYS 5.2 1.5 + - - -
186A GLY* 3.5 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO 3.6 15.4 + - - +
76A SER* 3.6 25.0 - - - +
78A ARG* 1.3 78.5 - - - +
80A ARG* 1.3 56.4 + - - +
82A LEU 3.6 0.3 + - - -
83A LEU* 2.4 47.1 + - + +
127A ALA* 3.4 29.2 - - - +
128A GLY* 4.9 2.1 - - - +
130A ALA* 4.1 3.6 - - + -
131A THR* 3.9 21.8 + - - +
121C GLN* 5.0 2.6 - - - +
124C ARG* 3.6 32.6 - - - +
125C TYR* 3.9 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A SER 3.3 16.8 + - - +
77A ALA* 3.5 8.5 + - - +
78A ARG 3.3 0.2 - - - -
79A GLU* 1.3 81.9 - - - +
81A ILE* 1.3 58.8 + - + +
82A LEU 3.3 0.2 - - - -
83A LEU* 3.8 20.0 - - - +
84A ARG* 2.7 83.4 + - - +
87A ASP* 4.6 5.9 + - - -
87C ASP* 3.4 24.1 + - - -
90C GLU* 5.0 4.6 + - - -
124C ARG* 3.3 36.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A TRP* 4.9 2.0 - - + -
73A MET* 3.8 24.7 - - + -
77A ALA 3.2 17.7 + - - +
78A ARG* 4.1 8.5 - - + +
79A GLU 3.4 0.4 - - - -
80A ARG* 1.3 78.1 - - + +
82A LEU* 1.3 67.8 + - + +
84A ARG 3.6 0.2 + - - -
85A LEU* 3.3 21.3 + - + +
208A ALA* 4.6 0.9 - - - +
211A ALA* 3.6 21.0 - - + +
212A GLY* 3.6 25.4 - - - +
213A LEU* 3.8 40.8 - - + +
214A PRO* 4.4 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 3.4 20.2 + - + +
79A GLU* 3.6 0.6 + - - -
80A ARG 3.3 0.2 - - - -
81A ILE* 1.3 86.5 - - + +
83A LEU* 1.3 57.4 + - - +
85A LEU* 4.0 6.0 - - + +
86A ALA* 3.3 24.9 + - - +
123A LEU* 3.8 32.7 - - + +
126A MET* 4.5 0.4 - - + -
127A ALA* 3.6 34.3 - - + +
130A ALA* 5.1 0.4 - - + -
179A ILE* 5.4 0.2 - - + -
180A ALA* 4.1 8.1 - - - +
183A LEU* 4.1 29.6 - - + -
184A ALA* 3.8 30.3 - - + +
213A LEU* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 2.4 50.1 + - + +
80A ARG* 3.7 17.9 - - - +
82A LEU* 1.3 72.9 - - - +
84A ARG* 1.3 63.0 + - - +
85A LEU 3.3 0.4 - - - -
86A ALA* 3.7 5.0 + - - +
87A ASP* 3.3 28.3 + - - +
124A ARG* 4.3 10.3 + - + +
127A ALA* 3.1 30.5 - - + -
83C LEU* 3.9 27.4 - - + -
124C ARG* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 2.7 72.3 + - - +
81A ILE 3.6 0.2 + - - -
82A LEU 3.5 0.2 - - - -
83A LEU* 1.3 75.6 - - - +
85A LEU* 1.3 57.7 + - - +
87A ASP* 3.4 10.4 - - - +
88A LEU* 3.2 26.2 + - + +
211A ALA* 4.0 31.6 + - + +
212A GLY* 5.8 1.8 - - - -
90C GLU* 5.8 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 3.3 18.4 + - + +
82A LEU* 3.8 5.8 + - + +
83A LEU 3.3 0.2 - - - -
84A ARG* 1.3 73.7 - - - +
86A ALA* 1.3 61.1 + - - +
87A ASP 3.0 1.6 - - - -
88A LEU* 2.9 5.3 + - + +
89A LEU* 2.9 35.7 + - + +
123A LEU* 4.1 24.2 - - + -
179A ILE* 5.1 6.3 - - + -
183A LEU* 6.4 0.9 - - + -
204A LEU* 4.3 15.3 - - + +
207A LEU* 3.1 48.9 - - + +
208A ALA* 3.4 17.5 - - + +
211A ALA* 3.8 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU 3.3 16.2 + - - +
83A LEU 4.0 2.2 - - - +
85A LEU* 1.3 78.1 - - - +
87A ASP* 1.3 59.6 + - - +
89A LEU* 3.5 1.7 + - - +
90A GLU* 3.4 23.0 + - - +
120A ALA* 3.5 32.4 - - - +
123A LEU* 3.9 14.4 - - + +
124A ARG* 3.7 29.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 4.6 5.5 + - - -
83A LEU* 3.3 14.9 + - - +
84A ARG* 3.4 15.3 - - - +
86A ALA* 1.3 80.3 - - - +
88A LEU* 1.3 55.2 + - - +
89A LEU 3.5 0.2 - - - -
90A GLU* 4.2 5.3 - - - +
91A VAL* 3.4 27.5 + - - +
124A ARG* 3.2 19.4 + - - +
80C ARG* 3.4 21.5 + - - -
87C ASP* 3.8 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 3.2 15.9 + - - +
85A LEU* 2.9 11.9 + - + +
87A ASP* 1.3 76.7 - - - +
89A LEU* 1.3 61.6 + - - +
90A GLU 3.3 0.9 - - - -
91A VAL* 4.0 11.7 - - + +
92A HIS* 3.4 38.6 - - + +
207A LEU* 3.6 36.1 - - + +
210A GLU* 3.7 38.1 - - + +
211A ALA* 3.9 9.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 2.9 21.3 + - + +
86A ALA* 3.5 5.8 + - - +
88A LEU* 1.3 79.0 - - - +
90A GLU* 1.3 61.5 + - - +
91A VAL 3.4 0.2 - - - -
92A HIS 3.8 1.5 - - - -
93A GLY* 3.4 12.6 + - - -
96A LEU* 3.8 15.3 - - + +
116A VAL* 3.2 28.1 - - - +
119A SER* 3.8 28.3 - - - -
120A ALA* 4.4 2.9 - - + +
123A LEU* 4.3 16.4 - - + -
172A LEU* 4.5 16.4 - - + -
176A VAL* 4.7 3.1 - - + -
204A LEU* 4.4 16.4 - - + -
207A LEU* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ALA 3.4 10.6 + - - +
87A ASP* 4.3 4.8 - - - +
89A LEU* 1.3 81.3 - - - +
91A VAL* 1.3 61.7 + - - +
92A HIS 3.3 0.4 - - - -
93A GLY* 3.9 6.8 + - - -
116A VAL* 4.4 12.3 - - + +
117A GLY* 5.0 7.5 - - - +
120A ALA* 4.1 14.6 - - + +
124A ARG* 3.2 27.3 + - - -
80C ARG* 5.0 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ASP 3.4 18.9 + - - +
88A LEU* 4.2 9.2 - - + -
89A LEU 3.4 0.2 - - - -
90A GLU* 1.3 78.1 - - - +
92A HIS* 1.3 83.9 + - + +
93A GLY 3.3 2.8 + - - -
----------------------------------------------------------
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