Contacts of the helix formed by residues 80 - 94 (chain A) in PDB entry 3HB8
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 PHE 80 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ARG* 4.2 1.0 + - - -
79A VAL* 1.3 70.1 - - - +
81A TRP* 1.3 66.5 + - - +
82A LYS* 3.8 19.3 - - + -
83A GLY* 3.0 31.7 + - - -
84A VAL* 3.1 12.5 + - - +
105A GLY 4.5 10.8 - - - -
106A VAL* 4.5 13.5 - - + -
107A LYS 5.5 1.1 - - - -
108A ILE* 4.2 23.1 - - + -
225A PHE* 3.3 19.7 - + + -
315A EDO 5.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A PHE* 3.7 25.1 - + - -
73A LEU* 4.3 23.1 - - + -
78A ARG* 6.1 1.6 - - - +
79A VAL* 2.7 15.2 + - - +
80A PHE* 1.3 70.0 - - - +
82A LYS* 1.3 59.6 + - - +
84A VAL* 2.7 51.4 + - + +
85A LEU* 2.9 42.5 + - + +
228A ALA* 4.6 0.2 - - + -
232A LEU* 4.0 25.1 - - + -
279A LEU* 4.0 10.8 - - + -
296A PHE* 4.8 3.8 - - + -
297A GLN* 5.5 2.2 - - - +
298A ILE* 3.3 46.0 - - + +
301A TYR* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.4 22.1 - - + -
81A TRP* 1.3 82.4 - - - +
83A GLY* 1.3 62.3 + - - +
85A LEU* 4.1 5.1 - - - +
86A GLU* 3.0 40.3 + - - +
104A LYS 2.9 30.3 + - - -
105A GLY* 3.8 17.3 - - - +
106A VAL* 4.4 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A PHE* 3.0 29.1 + - - -
82A LYS* 1.3 78.3 - - - +
84A VAL* 1.3 57.3 + - - +
87A GLU* 2.9 35.5 + - - +
106A VAL* 3.6 21.5 - - - +
225A PHE* 3.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A VAL* 4.3 3.6 - - + -
80A PHE 3.1 9.5 + - - +
81A TRP* 2.7 33.3 + - + +
83A GLY* 1.3 71.3 - - - +
85A LEU* 1.3 63.3 + - - +
87A GLU* 3.9 1.2 - - - +
88A LEU* 3.1 23.7 + - - +
225A PHE* 3.2 45.9 - - + +
228A ALA* 3.8 15.9 - - + -
229A SER* 3.6 33.7 + - - +
232A LEU* 4.3 5.2 - - + -
----------------------------------------------------------
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 TRP* 2.9 39.1 + - + +
82A LYS* 4.1 5.6 - - - +
84A VAL* 1.3 74.4 - - - +
86A GLU* 1.3 64.1 + - - +
88A LEU* 3.4 3.3 + - - +
89A LEU* 3.1 39.8 + - + +
232A LEU* 3.6 26.2 - - + -
236A MET* 5.7 0.2 - - - -
293A ALA* 3.6 29.4 - - + +
296A PHE* 3.4 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LYS* 3.0 28.5 + - - +
85A LEU* 1.3 74.7 - - - +
87A GLU* 1.3 68.1 + - - +
89A LEU* 3.2 19.5 + - - +
90A TRP* 2.9 21.8 + - - +
101A LEU* 4.0 7.9 - - + -
104A LYS* 3.2 62.6 + - + +
106A VAL* 3.7 13.0 - - + -
293A ALA* 4.1 21.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY 2.9 21.9 + - - +
84A VAL 3.9 1.1 - - - +
86A GLU* 1.3 76.3 - - - +
88A LEU* 1.3 63.0 + - - +
90A TRP* 2.9 26.5 - - + +
91A PHE* 2.9 41.5 + - + -
101A LEU* 3.8 13.1 - - + +
106A VAL* 5.2 0.2 - - + -
108A ILE* 3.5 17.2 - - + +
109A TRP* 3.0 28.3 + - + +
225A PHE* 3.7 17.5 - - - -
229A SER* 3.8 11.4 + - - -
314A UMP 5.7 0.7 - - - +
----------------------------------------------------------
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 VAL 3.1 18.3 + - - +
85A LEU 3.7 4.3 - - - +
86A GLU 3.2 0.4 - - - -
87A GLU* 1.3 77.3 + - - +
89A LEU* 1.3 55.6 + - - +
91A PHE* 2.8 31.3 + - + +
92A ILE* 2.9 23.2 + - + +
139A TRP* 3.8 31.0 - - + -
229A SER* 4.0 15.3 - - - +
230A TYR* 6.3 0.7 - - + -
232A LEU* 3.4 33.9 - - + -
233A LEU* 3.6 31.0 - - + +
236A MET* 3.7 15.5 - - - -
----------------------------------------------------------
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* 3.1 24.8 + - + +
86A GLU* 3.5 17.5 - - - +
88A LEU* 1.3 76.5 - - + +
90A TRP* 1.3 60.5 + - - +
92A ILE* 3.4 9.4 + - + +
93A LYS* 3.1 35.1 + - + +
236A MET* 4.5 13.0 - - + -
291A PHE* 3.9 34.8 - - + +
292A LYS* 4.1 1.8 - - - -
293A ALA* 3.5 37.5 - - + +
296A PHE* 4.5 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLU 2.9 13.1 + - - +
87A GLU* 2.9 18.2 - - + +
88A LEU 2.9 0.2 - - - -
89A LEU* 1.3 76.2 - - - +
91A PHE* 1.3 98.6 + + - +
93A LYS* 3.3 22.1 + - - +
95A SER* 2.9 59.5 + - - +
97A ASN 3.4 22.1 + - - -
98A ALA* 3.8 4.7 - - - -
100A GLU* 3.9 5.3 - - + +
101A LEU* 3.6 37.4 - - + +
109A TRP* 3.7 26.9 - + - -
131A LEU* 3.2 35.4 - - + -
134A VAL* 4.9 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A GLU* 2.9 50.2 + - - -
88A LEU* 2.8 18.7 + - + +
90A TRP* 1.3 101.5 - + - +
92A ILE* 1.3 60.8 + - - +
94A GLY* 2.9 21.1 + - - -
95A SER 5.4 0.4 - - - -
109A TRP* 4.3 2.7 - + - -
134A VAL* 5.8 0.7 - - + -
135A TYR* 3.4 47.8 - + + -
136A GLY* 3.5 18.3 - - - +
139A TRP* 3.5 40.2 - + + -
140A ARG* 4.4 1.7 - - - -
196A HIS* 6.3 2.0 - + - -
229A SER* 5.7 2.0 - - - -
230A TYR* 5.8 3.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 2.9 26.6 + - + +
89A LEU* 3.6 16.2 - - + +
90A TRP 3.2 0.4 - - - -
91A PHE* 1.3 75.9 - - - +
93A LYS* 1.3 56.0 + - + +
139A TRP* 4.5 7.0 - - + -
140A ARG* 2.6 50.8 + - - +
161A LEU* 3.7 21.8 - - + -
233A LEU* 5.1 3.4 - - + -
236A MET* 3.4 33.7 - - + -
288A ILE* 3.9 26.2 - - + +
289A ASP* 4.3 8.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.1 28.0 + - + +
90A TRP* 3.7 16.1 - - - +
91A PHE 3.2 0.4 - - - -
92A ILE* 1.3 75.1 - - + +
94A GLY* 1.3 58.1 + - - +
95A SER* 3.1 10.4 + - - +
100A GLU* 2.9 32.1 + - - +
104A LYS* 4.2 17.4 - - - +
140A ARG* 4.8 2.0 - - - +
141A HIS* 5.9 0.3 + - - -
289A ASP* 6.1 3.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A PHE 2.9 16.5 + - - -
92A ILE 3.0 2.3 - - - -
93A LYS* 1.3 79.5 - - - +
95A SER* 1.3 65.6 + - - +
96A THR* 3.5 11.4 + - - +
136A GLY* 3.8 16.6 - - - -
137A PHE* 3.9 7.7 + - - -
140A ARG* 4.5 8.5 - - - -
141A HIS* 5.3 8.5 - - - -
----------------------------------------------------------
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