Contacts of the helix formed by residues 80 - 92 (chain A) in PDB entry 3UGV
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 ALA 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO* 3.0 15.1 + - + +
79A LEU* 1.3 73.4 - - - +
81A PRO* 1.3 71.8 - - + -
82A ALA* 3.3 2.2 - - + -
83A GLU* 2.9 31.0 + - + +
84A ILE* 2.8 24.5 + - - +
116A LEU* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU 3.8 4.5 - - - +
80A ALA* 1.3 84.0 - - - +
82A ALA* 1.3 52.6 + - - +
84A ILE* 3.9 3.1 - - + +
85A TYR* 2.7 36.9 + - - +
109A ASP* 3.8 7.3 - - - +
112A VAL* 3.4 28.4 - - + +
113A TRP* 3.2 54.7 - - + +
116A LEU* 4.0 23.8 - - + -
285A SER* 4.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.0 1.4 + - - +
81A PRO* 1.3 77.1 - - - +
83A GLU* 1.3 66.6 + - + +
85A TYR* 3.5 8.9 + - - +
86A ASP* 3.2 20.8 + - - +
113A TRP* 5.1 4.2 - - + -
285A SER* 4.7 5.3 + - - +
289A ARG* 4.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PRO* 4.2 19.2 - - - +
80A ALA* 2.9 25.4 + - + +
82A ALA* 1.3 75.7 - - + +
84A ILE* 1.3 68.5 + - + +
86A ASP* 3.1 8.5 + - - +
87A LYS* 3.0 44.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PHE* 4.3 17.3 - - + -
74A LEU* 3.8 33.2 - - + -
77A GLN* 6.2 1.1 - - + -
78A PRO 3.7 22.9 - - - +
79A LEU* 4.0 7.0 - - - -
80A ALA 2.8 24.2 + - - +
81A PRO* 3.9 4.9 - - + +
83A GLU* 1.3 77.3 - - + +
85A TYR* 1.3 65.7 + - - +
87A LYS* 3.2 10.9 + - + +
88A THR* 3.0 27.5 + - + +
108A VAL* 3.8 18.6 - - + -
109A ASP* 5.8 1.8 - - - +
112A VAL* 4.1 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A PRO 2.7 23.0 + - - +
82A ALA* 3.6 8.1 - - - +
84A ILE* 1.3 74.4 - - - +
86A ASP* 1.3 63.4 + - - +
88A THR* 3.2 16.6 + - - -
89A ARG* 3.2 55.1 + - + +
102A MET* 4.0 15.3 - - + -
105A ALA* 4.9 3.8 - - + -
109A ASP* 3.9 24.9 - - + +
258A GLY* 5.3 0.2 - - - -
259A PRO* 4.7 6.8 - - - +
281A ILE 4.1 4.7 + - - -
282A GLY* 3.4 37.9 - - - -
285A SER* 4.2 6.1 - - - +
286A GLY* 4.3 7.5 - - - -
289A ARG* 3.3 35.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ALA 3.2 10.1 + - - +
83A GLU* 3.1 11.1 + - - +
85A TYR* 1.3 81.5 - - + +
87A LYS* 1.3 66.1 + - + +
89A ARG* 4.0 3.5 - - - +
90A LYS* 3.0 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.2 9.6 - - + +
74A LEU* 4.0 21.7 - - + +
77A GLN* 2.7 45.3 + - - +
78A PRO* 4.7 6.5 + - - +
83A GLU* 3.0 41.6 + - - +
84A ILE* 3.2 7.8 + - + +
86A ASP* 1.3 77.8 - - + +
88A THR* 1.3 60.2 + - - +
90A LYS* 4.0 4.7 - - - +
91A SER* 3.0 31.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 3.7 37.3 - - + +
73A MET* 4.1 7.9 - - + -
74A LEU* 4.0 24.5 - - + -
84A ILE* 3.0 25.2 + - + +
85A TYR* 3.2 11.4 + - - -
87A LYS* 1.3 75.0 - - - +
89A ARG* 1.3 63.0 + - - +
91A SER* 2.8 23.3 + - - -
92A LEU* 3.6 4.9 + - - +
105A ALA* 3.5 19.8 + - - +
108A VAL* 4.6 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A TYR* 3.2 53.3 + - + +
86A ASP* 4.0 3.8 - - - +
87A LYS 3.3 0.2 - - - -
88A THR* 1.3 78.0 + - - +
90A LYS* 1.3 67.0 + - + +
92A LEU* 3.1 6.3 + - - +
93A HIS 3.0 18.5 + - - -
96A GLY 5.5 0.2 - - - +
97A TYR* 3.2 67.0 + - + +
101A SER* 6.0 2.2 - - - -
102A MET* 3.9 19.7 - - + +
105A ALA* 4.5 12.3 - - + -
257A TYR 4.6 11.9 + - - -
258A GLY* 5.3 5.1 - - - -
259A PRO* 5.4 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASP* 3.0 49.1 + - - +
87A LYS* 4.0 4.7 - - - +
89A ARG* 1.3 77.3 - - + +
91A SER* 1.3 64.9 + - - +
92A LEU 2.9 0.9 + - - -
93A HIS* 2.9 33.0 + - + +
97A TYR* 4.0 18.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET* 4.7 5.5 - - - +
73A MET* 3.7 23.9 - - - +
87A LYS 3.0 17.0 + - - -
88A THR* 2.8 17.5 + - - -
90A LYS* 1.3 77.3 - - - +
92A LEU* 1.3 73.9 + - - +
93A HIS* 5.3 0.2 + - - -
94A PHE* 5.4 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ALA* 5.2 11.2 - - + -
70A MET* 3.9 20.4 - - + -
88A THR 3.6 4.5 + - - +
89A ARG* 3.1 8.2 + - - +
90A LYS 3.0 0.4 - - - -
91A SER* 1.3 98.3 + - - +
93A HIS* 1.3 63.8 + - - +
94A PHE* 3.2 3.8 - - - -
95A VAL* 3.0 29.6 + - + +
96A GLY 3.3 11.0 + - - +
100A LEU 5.4 0.4 - - - +
101A SER* 3.9 35.9 - - - +
104A ALA* 5.6 0.4 - - + -
----------------------------------------------------------
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