Contacts of the helix formed by residues 74 - 88 (chain B) in PDB entry 5M7R
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 VAL 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ARG* 6.2 2.5 - - + -
72B PRO 4.4 7.0 - - - +
73B TRP* 1.3 79.0 - - - +
75B MET* 1.3 68.5 + - - +
76B GLU* 4.4 12.1 - - + +
77B GLN* 3.1 29.6 + - + +
78B ARG* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 1.3 75.7 - - - +
76B GLU* 1.3 63.5 + - - +
78B ARG* 3.3 29.8 + - - +
79B LYS* 3.0 43.9 + - - +
95B TYR* 5.7 0.9 - - + -
115B GLU 5.5 0.2 - - - +
118B GLN* 3.8 43.5 - - + +
119B LEU* 4.6 15.3 - - + +
122B LEU* 3.7 33.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B VAL* 3.3 10.7 - - + +
75B MET* 1.3 78.1 - - - +
77B GLN* 1.3 60.2 + - + +
79B LYS* 3.5 11.8 + - - +
80B GLU* 3.0 27.9 + - + +
395B HIS* 4.1 21.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B PRO 4.8 0.3 - - - +
73B TRP* 3.4 14.6 - - + +
74B VAL* 3.1 40.1 + - + +
76B GLU* 1.3 78.3 - - + +
78B ARG* 1.3 60.1 + - - +
80B GLU* 3.1 6.8 + - - +
81B LEU 2.7 26.5 + - - -
318B PHE* 3.3 56.7 - - + +
319B GLU* 5.4 2.4 + - - +
635B THR* 5.9 4.2 - - - +
639B ASP* 4.7 6.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 2.8 42.4 + - - +
72B PRO* 3.9 1.8 - - - +
73B TRP* 3.1 26.9 + - + -
74B VAL* 3.1 15.8 + - - +
75B MET* 3.3 36.0 + - - +
77B GLN* 1.3 76.5 - - - +
79B LYS* 1.3 62.8 + - - +
81B LEU* 3.1 12.0 + - - +
82B PHE* 3.1 32.5 + - + -
93B TYR* 3.4 14.2 + - + +
95B TYR* 3.6 22.8 - - - -
97B PRO* 3.7 3.0 - - - +
100B ASP* 3.2 23.6 + - - -
122B LEU* 3.6 27.8 - - + +
318B PHE* 5.1 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B MET* 3.0 41.7 + - - +
76B GLU* 3.7 8.5 - - - +
78B ARG* 1.3 73.4 - - - +
80B GLU* 1.3 64.3 + - - +
82B PHE* 3.0 22.9 + - - +
83B ARG* 3.3 10.9 + - - +
118B GLN* 4.2 8.7 + - - -
121B THR* 3.9 33.7 - - - +
122B LEU* 4.1 20.8 - - + +
125B ALA* 4.0 22.0 - - + -
129B TYR* 4.1 9.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 3.0 16.1 + - + +
77B GLN* 3.5 9.9 - - - +
79B LYS* 1.3 76.5 - - - +
81B LEU* 1.3 62.1 + - - +
83B ARG* 2.5 46.9 + - - +
84B ARG* 2.9 53.8 + - - +
318B PHE* 4.1 8.7 - - + -
319B GLU* 5.4 1.3 - - - +
395B HIS* 6.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B VAL* 4.0 11.0 - - + -
73B TRP* 3.9 24.9 - - + -
77B GLN 2.7 15.8 + - - +
78B ARG* 3.1 12.1 + - - +
80B GLU* 1.3 72.9 - - - +
82B PHE* 1.3 59.5 + - + +
84B ARG* 3.0 13.4 + - + +
85B LEU* 2.8 48.5 + - + +
93B TYR* 3.7 31.4 - - + -
318B PHE* 3.8 18.3 - - + -
325B ILE* 3.7 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 3.1 16.0 + - + -
79B LYS* 3.0 13.9 + - - +
81B LEU* 1.3 77.9 - - + +
83B ARG* 1.3 58.1 + - - +
85B LEU* 3.4 6.6 + - + +
86B GLN* 2.9 30.3 + - - +
93B TYR* 3.6 48.2 - + + -
122B LEU* 3.4 48.7 - - + -
125B ALA* 3.9 5.2 - - + -
126B ALA* 3.6 28.0 - - + -
129B TYR* 3.7 20.0 - - + +
131B ILE* 3.8 24.0 - - + +
133B PHE* 4.2 1.3 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS 3.3 6.8 + - - +
80B GLU* 2.5 52.2 + - - +
81B LEU 3.2 0.2 - - - -
82B PHE* 1.3 80.2 - - - +
84B ARG* 1.3 65.9 + - - +
86B GLN* 3.4 3.0 + - - +
87B LYS* 3.0 63.1 + - - +
129B TYR* 3.7 38.3 - - + +
390B GLU* 5.7 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B GLU* 2.9 43.4 + - - +
81B LEU* 3.0 16.2 + - + +
83B ARG* 1.3 81.6 - - - +
85B LEU* 1.3 67.4 + - - +
87B LYS* 3.3 7.4 + - + +
88B TRP* 2.9 65.1 + - + -
318B PHE* 4.1 18.3 + - - -
319B GLU* 3.0 39.6 + - - +
321B ASN 5.4 1.0 - - - -
322B TYR* 3.6 36.6 - - + +
325B ILE* 6.1 1.6 - - - -
390B GLU* 5.6 6.8 + - - +
395B HIS* 6.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY* 4.4 3.8 - - - -
64B VAL* 4.0 14.4 - - + -
81B LEU* 2.8 40.3 + - + +
82B PHE* 3.7 6.5 - - + +
84B ARG* 1.3 78.2 - - - +
86B GLN* 1.3 63.0 + - - +
88B TRP* 3.3 3.4 + - - -
89B GLU 3.1 4.2 + - - -
90B LEU* 2.9 58.6 + - + +
92B THR 3.9 19.5 - - - +
93B TYR* 4.6 2.5 - - + -
131B ILE* 3.6 28.9 - - + -
325B ILE* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE 2.9 15.8 + - - +
83B ARG* 3.8 4.8 - - - +
85B LEU* 1.3 76.6 - - - +
87B LYS* 1.3 64.3 + - - +
89B GLU* 2.9 17.7 + - - +
90B LEU 4.3 3.1 - - - -
128B GLU 4.7 2.7 + - - +
129B TYR* 3.3 51.1 + - + +
130B GLU* 3.2 28.0 + - + +
131B ILE* 3.9 6.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ARG* 3.0 42.7 + - + +
84B ARG* 3.5 6.1 - - + +
86B GLN* 1.3 81.4 - - - +
88B TRP* 1.3 74.2 + - + +
89B GLU* 3.5 6.8 + - - +
322B TYR* 4.3 7.5 + - - -
386B GLU* 3.6 29.7 + - - +
390B GLU* 5.0 6.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ARG* 2.9 56.1 + - + +
85B LEU* 4.3 2.5 - - - +
87B LYS* 1.3 92.7 - - + +
89B GLU* 1.3 69.9 + - - +
90B LEU* 3.4 2.9 - - + -
321B ASN 5.3 0.2 - - - -
322B TYR* 3.5 49.4 - + - -
325B ILE* 3.6 39.9 - - + -
326B HIS* 3.5 28.9 - + - -
329B ALA* 3.5 23.4 - - + +
333B LYS* 3.2 24.5 + - - +
386B GLU* 3.0 21.5 + - - -
----------------------------------------------------------
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