Contacts of the helix formed by residues 77 - 94 (chain B) in PDB entry 4F4W
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 ARG 77 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B GLU* 2.7 40.6 + - - +
19B LEU* 3.7 20.6 - - - +
20B ASN* 3.6 15.0 + - - +
75B PRO* 3.8 14.8 + - + +
76B MET* 1.3 76.2 - - - +
78B LYS* 1.3 66.1 + - - +
79B PRO* 3.2 8.1 - - + -
80B ILE* 3.0 43.1 + - + +
81B TYR* 3.0 24.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PHE* 4.8 15.3 - - + -
76B MET* 3.6 32.9 + - + +
77B ARG* 1.3 73.9 - - - +
79B PRO* 1.3 71.9 - - + +
81B TYR* 3.1 11.6 + - + -
82B GLU* 2.9 52.7 + - + +
104B ILE* 4.8 9.4 - - + -
6F G 5.9 0.2 + - - -
7F C 4.8 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 3.3 7.4 - - + -
78B LYS* 1.3 93.9 - - + +
80B ILE* 1.3 62.9 + - + +
82B GLU* 3.4 14.9 + - - +
83B ALA* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 4.2 6.1 - - + -
16B GLU* 5.5 0.2 - - - +
19B LEU* 4.0 17.7 - - + -
77B ARG* 3.0 55.9 + - + +
79B PRO* 1.3 79.4 - - + +
81B TYR* 1.3 67.7 + - + +
83B ALA* 3.1 8.6 + - + +
84B PHE* 3.0 43.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.6 10.1 - - + -
12B PHE* 3.2 72.0 - + + -
15B VAL* 3.7 23.6 - - + -
16B GLU* 2.5 38.0 + - + +
30B VAL* 3.8 9.5 - - - +
75B PRO 3.8 0.2 + - - -
76B MET* 3.8 7.4 - - + -
77B ARG* 3.0 38.3 + - + -
78B LYS* 3.1 11.6 + - - +
80B ILE* 1.3 77.9 - - + +
82B GLU* 1.3 57.8 + - - +
84B PHE* 3.3 7.0 + - - +
85B SER* 2.8 30.7 + - - -
104B ILE* 4.2 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 2.9 51.2 + - + +
79B PRO* 3.6 14.0 - - - +
81B TYR* 1.3 75.9 - - - +
83B ALA* 1.3 52.3 + - - +
85B SER* 3.3 3.3 + - - -
86B ASN* 2.8 48.5 + - - +
104B ILE* 3.8 21.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PRO 3.1 13.9 + - - +
80B ILE* 3.1 12.8 + - + +
82B GLU* 1.3 74.3 - - - +
84B PHE* 1.3 67.0 + - + +
86B ASN* 3.3 9.2 + - - +
87B ARG* 3.0 43.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.0 12.6 - - + -
15B VAL* 3.6 32.8 - - + -
18B VAL* 4.1 12.3 - - + -
19B LEU* 3.8 26.9 - - + -
80B ILE* 3.0 30.8 + - + +
81B TYR 3.6 7.2 - - - +
83B ALA* 1.3 75.4 - - + +
85B SER* 1.3 63.9 + - - +
87B ARG* 3.2 28.8 + - - +
88B ILE* 3.0 30.8 + - + +
137B GLU* 3.8 33.7 - - + -
139B ILE* 4.1 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 4.3 6.3 - - - -
11B PHE* 4.0 7.8 - - - -
81B TYR 2.8 17.8 + - - -
82B GLU* 3.5 4.7 - - - -
83B ALA 3.2 0.2 - - - -
84B PHE* 1.3 77.6 - - - +
86B ASN* 1.3 66.1 + - - +
88B ILE* 3.1 2.9 + - - +
89B MET* 2.9 35.4 + - - +
101B VAL* 5.8 0.5 - - - +
104B ILE* 2.5 45.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU* 2.8 34.1 + - - +
83B ALA* 3.7 8.0 - - - +
84B PHE 3.3 0.2 - - - -
85B SER* 1.3 78.1 + - - +
87B ARG* 1.3 61.4 + - + +
89B MET* 3.6 6.8 + - - +
90B ASN* 3.1 34.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ALA* 3.0 42.2 + - - +
84B PHE* 3.6 34.9 - - - +
86B ASN* 1.3 76.0 - - + +
88B ILE* 1.3 63.1 + - - +
90B ASN* 3.3 10.7 + - - +
91B LEU* 3.0 26.9 + - + +
137B GLU* 2.8 44.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.3 41.7 - - + -
11B PHE* 4.7 3.8 - - + -
84B PHE* 3.0 21.3 + - + +
85B SER 3.7 2.5 - - - +
87B ARG* 1.3 73.7 - - - +
89B MET* 1.3 66.3 + - - +
91B LEU* 2.9 10.7 + - + +
92B LEU* 2.9 24.4 + - + +
133B ILE* 3.9 31.0 - - + -
137B GLU* 4.0 18.8 - - + -
139B ILE* 4.1 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.5 26.7 - - + -
85B SER* 2.9 26.6 + - - +
86B ASN* 4.0 6.5 - - - +
88B ILE* 1.3 72.4 - - - +
90B ASN* 1.3 60.4 + - - +
92B LEU* 3.3 24.9 + - - +
93B ASN* 2.9 30.0 + - - +
99B ILE* 4.1 3.3 - - + +
101B VAL* 3.9 26.9 - - + -
103B SER 3.8 11.0 - - - +
104B ILE 3.9 4.5 - - - +
106B GLU 3.7 33.9 - - - +
107B ALA* 3.8 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN* 3.1 24.2 + - - +
87B ARG* 3.5 11.8 - - - +
89B MET* 1.3 76.5 - - - +
91B LEU* 1.3 67.1 + - + +
93B ASN* 3.5 17.7 + - - +
94B LYS* 3.8 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.0 15.9 + - + +
88B ILE* 2.9 13.8 + - + +
90B ASN* 1.3 76.8 - - + +
92B LEU* 1.3 66.0 + - + +
94B LYS* 3.3 24.6 + - - +
95B HIS* 3.2 20.2 + - + -
132B GLU* 3.8 28.9 - - + +
133B ILE* 4.6 18.8 - - + -
136B LYS* 3.9 37.0 - - + -
137B GLU* 4.7 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B VAL* 4.0 25.1 - - + -
8B PHE* 4.6 2.0 - - + -
88B ILE* 2.9 24.3 + - + +
89B MET* 3.5 33.9 - - - +
91B LEU* 1.3 76.3 - - - +
93B ASN* 1.3 62.9 + - - +
95B HIS* 2.8 21.6 + - + +
96B ALA 3.5 6.1 + - - -
99B ILE* 3.8 11.2 - - + -
107B ALA* 4.2 13.7 - - + -
109B LEU* 3.7 16.8 - - + +
129B ILE* 3.4 33.2 - - + -
133B ILE* 3.9 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B MET 2.9 17.4 + - - +
90B ASN* 3.7 12.2 + - - +
91B LEU 3.2 0.6 - - - -
92B LEU* 1.3 75.1 - - - +
94B LYS* 1.3 63.1 + - - +
96B ALA* 3.3 20.4 + - - +
98B LYS* 5.8 0.3 - - - -
99B ILE* 3.3 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ASN 3.8 5.9 + - - +
91B LEU* 3.4 37.3 + - - +
92B LEU 2.9 0.4 + - - -
93B ASN* 1.3 84.1 - - - +
95B HIS* 1.3 67.4 + - + +
96B ALA 3.4 1.2 + - - +
114B LYS* 2.9 23.7 + - - -
132B GLU* 4.5 6.7 + - - -
----------------------------------------------------------
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