Contacts of the helix formed by residues 78 - 92 (chain W) in PDB entry 1MVW
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 ASN 78 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68W LYS* 5.7 0.8 - - - +
70W PRO* 3.2 16.6 + - + +
76W ILE* 4.0 3.1 - - - +
77W THR* 1.3 80.7 - - + +
79W TRP* 1.3 62.3 + - - +
80W ASP* 3.3 16.9 + - - +
81W ASP* 3.0 45.1 + - + +
82W MET* 3.1 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76W ILE* 3.8 51.1 + - + -
77W THR 4.6 6.9 + - - -
78W ASN* 1.3 73.3 + - - +
80W ASP* 1.3 61.8 + - - +
82W MET* 3.8 4.5 - - + +
83W GLU* 3.3 26.3 + - - +
86W TRP* 4.6 5.8 - + - -
115W ASN* 3.6 53.1 + - + -
118W LYS* 3.8 30.9 - - + +
119W MET* 3.8 22.4 - - + -
122W ILE* 3.6 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 80 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W ARG* 3.3 14.3 + - - -
78W ASN* 3.3 14.4 + - - +
79W TRP* 1.3 76.3 - - - +
81W ASP* 1.3 87.3 + - - +
83W GLU* 3.6 8.1 + - - +
84W LYS* 3.3 36.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 81 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W VAL* 3.4 19.6 - - + +
37W ARG* 2.9 27.0 + - - -
68W LYS* 3.1 31.7 - - - +
70W PRO* 3.4 19.4 - - + +
78W ASN* 3.0 27.1 + - + +
80W ASP* 1.3 88.9 + - - +
82W MET* 1.3 60.8 + - - +
84W LYS* 3.5 9.8 - - - +
85W ILE* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12W ASN* 3.5 26.9 - - + +
17W VAL* 5.8 0.4 - - + -
33W SER* 5.3 1.3 - - - +
70W PRO* 3.9 11.7 - - - -
71W ILE* 3.7 35.2 - - + -
76W ILE* 3.8 20.2 - - + -
78W ASN 3.1 17.0 + - - +
79W TRP* 3.6 6.9 + - + +
80W ASP 3.3 0.6 - - - -
81W ASP* 1.3 70.1 - - - +
83W GLU* 1.3 58.6 + - - +
84W LYS 3.0 1.1 - - - -
85W ILE* 2.7 45.0 + - + +
86W TRP* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79W TRP 3.3 15.8 + - - +
80W ASP* 3.8 7.4 - - - +
81W ASP 3.5 0.2 - - - -
82W MET* 1.3 76.4 - - - +
84W LYS* 1.3 56.9 + - - +
86W TRP* 3.9 13.8 - - + -
87W HIS* 2.9 32.0 + - + +
122W ILE* 4.1 20.7 - - + +
126W THR* 4.2 26.3 + - - +
127W PHE* 3.7 16.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 84 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35W VAL* 4.0 9.4 - - + -
37W ARG* 3.4 35.4 - - - +
51W ASP* 5.2 5.9 + - - +
52W SER* 3.5 26.2 - - - +
54W VAL* 4.4 10.5 - - + +
80W ASP* 3.3 25.9 + - - +
81W ASP* 3.5 25.8 - - - +
82W MET 3.0 0.2 - - - -
83W GLU* 1.3 78.9 - - - +
85W ILE* 1.4 61.8 + - - +
87W HIS* 3.2 7.5 + - + +
88W HIS* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17W VAL* 3.7 29.2 - - + -
31W PHE* 4.2 10.9 - - + -
33W SER* 3.9 27.1 - - - +
34W ILE 4.1 0.7 - - - +
35W VAL* 3.8 12.3 - - + -
54W VAL* 4.0 14.1 - - + -
70W PRO* 3.6 35.7 - - + -
81W ASP 3.3 7.2 + - - +
82W MET* 2.7 27.9 + - + +
84W LYS* 1.4 69.8 - - - +
86W TRP* 1.3 55.4 + - + +
88W HIS* 3.3 3.8 + - - +
89W THR* 2.7 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 86 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W CYS* 4.0 16.5 - - - -
12W ASN* 2.9 36.7 + - - +
17W VAL* 6.1 0.2 - - + -
76W ILE* 4.2 10.1 - - + -
79W TRP* 4.6 1.8 - + - -
82W MET* 2.9 39.5 + - + +
83W GLU* 3.8 18.2 - - - +
85W ILE* 1.3 74.0 - - + +
87W HIS* 1.3 59.4 + - - +
89W THR* 2.8 23.5 + - - -
90W PHE* 3.0 26.9 + + + -
105W LEU* 4.4 3.8 - - + +
119W MET* 3.9 29.8 - - + -
122W ILE* 4.1 24.2 - - + -
123W MET* 3.3 29.6 - - + +
127W PHE* 3.6 20.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D LYS* 3.5 28.6 + - - -
83W GLU* 2.9 20.1 + - + +
84W LYS* 3.4 7.9 - - - +
86W TRP* 1.3 75.9 - - - +
88W HIS* 1.3 60.9 + - - +
90W PHE* 4.5 0.4 - - - -
91W TYR* 2.9 65.4 + + + +
92W ASN* 4.6 6.2 + - - -
127W PHE* 3.9 16.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 88 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31W PHE* 3.6 20.7 - + - -
54W VAL* 3.9 38.3 + - + +
55W GLY* 5.2 0.6 - - - -
84W LYS 3.1 9.6 + - - +
85W ILE 3.4 8.3 - - - +
87W HIS* 1.3 78.9 - - - +
89W THR* 1.3 63.0 + - - +
92W ASN* 2.8 55.5 + - + -
93W GLU* 2.9 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10W CYS* 4.7 9.2 - - + -
17W VAL* 4.5 7.5 - - + +
19W ALA* 3.6 31.4 - - + -
31W PHE* 3.7 19.7 - - + -
85W ILE* 2.7 26.6 + - - +
86W TRP* 2.8 14.5 + - - -
88W HIS* 1.3 77.1 - - - +
90W PHE* 1.3 63.3 + - + -
93W GLU* 3.4 8.8 - - + +
94W LEU* 2.9 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8W LEU* 4.0 28.5 - - + -
10W CYS* 5.8 5.6 - - + -
86W TRP* 3.0 29.2 + + + +
87W HIS* 4.1 2.5 - - - +
89W THR* 1.3 83.1 - - + +
91W TYR* 1.3 62.9 + + + +
94W LEU* 3.5 4.7 - - + -
95W ARG 2.8 26.2 + - - -
96W VAL* 3.1 23.7 + - + +
98W PRO* 3.9 27.4 - - + -
103W THR* 4.4 15.3 - - + -
105W LEU* 6.1 0.4 - - + -
123W MET* 4.1 23.6 - - + -
127W PHE* 3.6 44.6 - + - -
129W VAL* 4.8 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 91 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87W HIS* 2.9 61.7 + + - +
90W PHE* 1.3 83.1 - - + +
92W ASN* 1.3 70.9 + - - +
95W ARG* 3.4 17.3 - - - +
96W VAL 3.8 12.3 - - - -
97W ALA* 4.6 4.9 - - + -
98W PRO* 3.7 34.8 - - + +
99W GLU* 4.2 11.2 + - - -
127W PHE* 4.9 9.2 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 92 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567D LYS* 6.0 1.8 - - - +
87W HIS* 4.2 7.8 + - - +
88W HIS* 2.8 48.9 + - + +
91W TYR* 1.3 93.9 + - - +
93W GLU* 1.3 68.2 + - - +
95W ARG* 3.3 17.5 - - - +
----------------------------------------------------------
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