Contacts of the helix formed by residues 78 - 93 (chain A) in PDB entry 2H3W
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 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU 4.9 0.7 - - - -
73A PHE 4.8 2.0 - - - -
75A THR* 2.9 29.5 + - - -
76A SER 3.2 0.8 - - - -
77A GLY* 1.3 80.0 - - - +
79A VAL* 1.3 65.3 + - - +
80A GLY 3.5 1.6 - - - -
81A GLU* 3.8 5.2 + - - +
82A ARG* 3.1 30.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A GLU 5.2 0.8 + - - -
73A PHE* 4.1 14.0 + - + +
78A GLY* 1.3 69.6 - - - -
80A GLY* 1.3 68.7 + - - +
82A ARG* 3.1 24.4 + - + +
83A LEU* 3.0 46.5 + - + +
532A VAL* 5.3 7.2 - - + -
533A SER 5.7 1.1 - - - +
535A PRO* 4.1 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.5 9.9 - - - +
73A PHE* 2.9 52.3 + - - -
79A VAL* 1.3 75.0 - - - +
81A GLU* 1.3 56.9 + - - +
83A LEU* 3.3 3.5 + - - +
84A GLN* 2.8 31.2 + - - +
523A LEU* 4.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 3.7 12.0 - - + +
73A PHE 4.0 2.6 + - - -
74A GLN* 5.1 3.2 - - - +
75A THR 4.4 4.9 - - - +
76A SER* 3.9 11.5 + - - -
77A GLY* 2.6 35.2 + - - -
78A GLY 3.8 11.6 + - - +
79A VAL 3.2 0.6 - - - -
80A GLY* 1.3 75.4 - - - +
82A ARG* 1.3 59.3 + - + +
84A GLN* 3.4 4.4 + - - +
85A LYS* 3.0 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 2.9 27.6 + - - -
78A GLY* 3.1 23.8 + - - +
79A VAL* 3.1 25.2 + - - +
81A GLU* 1.3 76.9 - - + +
83A LEU* 1.3 69.0 + - + +
85A LYS* 3.3 10.0 + - - +
86A GLY* 3.0 18.5 + - - -
89A ARG* 4.9 2.3 + - - -
530A ASP* 4.6 5.7 - - - +
532A VAL* 6.3 1.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
73A PHE* 3.9 22.7 - - + -
79A VAL* 3.0 34.5 + - + +
80A GLY 3.7 5.6 - - - +
82A ARG* 1.3 77.4 - - + +
84A GLN* 1.3 63.0 + - - +
86A GLY* 3.0 3.8 + - - -
87A LEU* 3.0 20.8 + - - +
523A LEU* 3.5 31.6 - - + +
526A GLN* 3.6 11.3 - - + +
527A ALA* 3.5 31.2 - - + +
530A ASP* 3.7 14.8 - - + +
532A VAL* 4.5 8.1 - - + -
535A PRO* 4.0 11.9 - - + -
538A PHE* 4.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 3.6 13.4 - - - +
41A PRO 3.0 20.6 - - - +
42A PRO* 4.1 2.3 - - - +
43A LEU* 3.6 26.6 + - + +
80A GLY 2.8 17.5 + - - +
81A GLU* 3.5 8.7 - - - +
83A LEU* 1.3 77.0 - - - +
85A LYS* 1.3 63.0 + - + +
87A LEU* 3.1 5.3 + - - +
88A GLU* 3.0 45.0 + - - +
519A HIS* 2.8 32.5 + - - -
523A LEU* 3.7 9.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A GLU* 3.0 37.4 + - + +
82A ARG* 3.5 11.0 - - - +
83A LEU 3.3 0.2 - - - -
84A GLN* 1.3 77.3 - - + +
86A GLY* 1.3 63.3 + - - +
88A GLU* 3.3 21.1 + - - +
89A ARG* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG 3.0 10.4 + - - -
83A LEU 3.0 7.8 + - - -
85A LYS* 1.3 77.6 - - - +
87A LEU* 1.3 56.2 + - - +
89A ARG* 3.2 27.4 + - - +
90A ARG* 2.9 27.4 + - - +
526A GLN* 3.6 20.4 + - - +
530A ASP* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.0 17.8 - - + +
83A LEU 3.0 13.6 + - - +
84A GLN* 3.1 8.3 + - - +
86A GLY* 1.3 75.7 - - - +
88A GLU* 1.3 58.3 + - - +
90A ARG* 3.1 8.1 + - - +
91A ALA* 2.9 28.1 + - - +
97A TRP* 4.1 14.5 - - + +
101A TRP* 3.5 32.1 - - + -
519A HIS* 3.7 24.0 - - + +
522A GLY* 3.6 14.8 - - - +
523A LEU* 3.4 37.0 - - + +
526A GLN* 3.9 7.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A VAL* 4.4 15.6 - - + +
84A GLN* 3.0 36.2 + - - +
85A LYS* 3.7 32.3 + - - +
87A LEU* 1.3 76.9 - - - +
89A ARG* 1.3 60.6 + - + +
91A ALA* 3.5 8.4 + - - +
92A LYS* 3.2 29.5 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
82A ARG 4.9 2.2 + - - -
85A LYS* 3.0 34.8 + - - +
86A GLY* 3.5 24.2 + - - +
87A LEU 3.2 0.2 - - - -
88A GLU* 1.3 74.5 - - + +
90A ARG* 1.3 66.3 + - - +
92A LYS* 3.0 32.2 + - - +
93A LYS* 3.2 27.1 + - + +
526A GLN* 4.8 6.5 - - - +
530A ASP* 5.0 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A GLY 2.9 14.3 + - - +
87A LEU* 3.1 11.4 + - - +
89A ARG* 1.3 78.4 - - - +
91A ALA* 1.3 60.9 + - - +
93A LYS* 3.3 19.3 + - - +
94A MET* 3.3 58.7 + - - +
97A TRP* 2.9 31.3 + - + -
100A GLU* 5.1 6.7 + - - +
101A TRP* 3.2 61.4 - - - +
526A GLN* 4.3 3.6 - - - +
529A GLU* 3.2 31.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
37A ARG* 5.6 6.1 - - - +
38A LEU 4.7 6.1 - - - +
40A VAL* 4.2 8.5 - - + -
87A LEU 2.9 15.0 + - - +
88A GLU* 3.7 7.4 - - - +
89A ARG 3.2 0.2 - - - -
90A ARG* 1.3 76.2 - - - +
92A LYS* 1.3 59.1 + - + +
93A LYS 3.4 0.2 - - - -
94A MET 3.2 19.3 - - - +
97A TRP* 3.8 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.2 19.5 - - + +
89A ARG* 3.0 25.1 + - - +
91A ALA* 1.3 79.8 - - + +
93A LYS* 1.3 58.2 + - + +
94A MET 3.5 0.9 - - - -
----------------------------------------------------------
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 ARG* 3.2 22.9 + - + +
90A ARG* 3.3 31.4 + - - +
92A LYS* 1.3 77.8 - - - +
94A MET* 1.3 67.0 + - + +
529A GLU* 5.3 7.3 + - - -
----------------------------------------------------------
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