Contacts of the helix formed by residues 79 - 97 (chain B) in PDB entry 4YCV
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 ASP 79 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B GLU 4.0 0.2 + - - -
78B VAL* 1.3 74.2 - - - +
80B PRO* 1.3 72.5 - - + +
81B ARG* 3.3 5.8 + - + +
82B LEU* 3.6 24.6 + - + +
83B TYR* 3.3 20.2 + - - +
220B MET* 4.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL 3.7 6.0 - - - +
79B ASP* 1.3 85.3 - - + +
81B ARG* 1.3 64.4 + - - +
83B TYR* 3.1 5.5 + - + +
84B PHE* 3.0 24.0 + - - +
219B HIS* 5.7 0.7 + - - -
220B MET* 4.1 26.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP* 3.3 4.4 - - + -
80B PRO* 1.3 79.6 - - + +
82B LEU* 1.3 59.2 + - - +
84B PHE* 3.2 13.4 - - - +
85B GLU* 3.0 24.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASP* 3.6 25.1 + - + +
80B PRO 3.4 0.2 - - - -
81B ARG* 1.3 76.8 - - - +
83B TYR* 1.3 63.6 + - - +
85B GLU* 3.7 19.5 - - - +
86B ASN* 2.8 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 5.5 8.7 - - + -
79B ASP 3.3 13.8 + - - +
80B PRO* 3.1 14.2 + - + +
82B LEU* 1.3 80.0 - - - +
84B PHE* 1.3 64.4 + - - +
86B ASN* 3.1 8.8 + - + +
87B ARG* 3.0 28.5 + - + +
185B ARG* 3.9 42.1 + - - +
186B ARG* 4.7 9.5 + - - +
217B CYS 5.0 5.3 + - - -
218B LEU 3.8 10.5 - - - -
219B HIS* 3.8 5.8 - - - -
220B MET* 3.7 49.0 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
512A PHE* 5.7 4.0 - + - -
544A GLU* 3.8 31.9 - - - -
80B PRO 3.0 12.1 + - - +
81B ARG* 3.2 13.5 - - - +
83B TYR* 1.3 77.9 - - - +
85B GLU* 1.3 65.1 + - + +
87B ARG* 3.4 1.4 + - - +
88B SER* 3.0 36.0 + - - -
218B LEU* 3.3 54.6 - - + +
219B HIS* 4.0 20.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG 3.0 15.5 + - - +
82B LEU* 3.8 16.7 - - - +
84B PHE* 1.3 79.6 - - + +
86B ASN* 1.3 67.3 + - - +
88B SER* 3.1 7.7 + - - -
89B LYS* 2.9 27.1 + - + +
----------------------------------------------------------
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 LEU* 2.8 42.0 + - - +
83B TYR* 3.3 11.2 - - + +
85B GLU* 1.3 80.4 - - - +
87B ARG* 1.3 57.6 + - - +
89B LYS* 3.5 7.0 - - - +
90B PHE* 2.9 23.6 + - - +
185B ARG* 5.2 5.4 - - - +
----------------------------------------------------------
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 TYR* 3.0 21.5 + - + +
84B PHE 4.3 1.6 - - - +
86B ASN* 1.3 75.5 - - - +
88B SER* 1.3 62.0 + - - +
90B PHE* 3.5 24.3 - - + -
91B ILE* 2.9 33.5 + - + +
183B LYS* 4.1 11.7 + - - +
185B ARG* 3.3 38.2 + - - +
186B ARG 5.1 0.8 + - - -
188B ASP* 2.3 51.8 + - - -
213B LEU* 3.6 16.6 - - - +
216B ALA* 3.4 21.9 - - - +
217B CYS 3.0 21.5 + - - -
218B LEU* 4.5 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PHE* 3.5 34.4 - - - -
84B PHE* 3.0 34.3 + - - -
85B GLU* 3.1 10.9 + - - -
87B ARG* 1.3 76.4 - - - +
89B LYS* 1.3 64.1 + - - +
91B ILE* 3.0 14.5 + - - +
92B GLN* 3.1 14.0 + - - +
218B LEU* 4.1 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU* 2.9 14.8 + - + +
86B ASN* 3.5 12.1 - - - +
88B SER* 1.3 77.4 - - - +
90B PHE* 1.3 60.9 + - - +
92B GLN* 3.5 2.8 + - - +
93B ASP* 2.9 39.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ASN 2.9 16.2 + - - +
87B ARG* 3.3 34.1 - - + +
89B LYS* 1.3 76.4 - - - +
91B ILE* 1.3 75.8 + - + +
93B ASP* 3.3 7.1 + - - +
94B GLN* 2.9 60.4 + - + +
101B PRO* 6.1 0.4 - - + -
183B LYS* 3.2 46.4 - - + -
185B ARG* 4.6 13.7 - - - +
213B LEU* 4.7 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PHE* 3.7 17.7 - - + -
87B ARG* 2.9 24.8 + - - +
88B SER 3.0 7.8 + - - +
90B PHE* 1.3 92.7 - - + +
92B GLN* 1.3 60.4 + - - +
94B GLN* 3.1 8.1 + - - +
95B LYS* 2.9 50.2 + - - +
101B PRO* 3.8 23.2 - - + +
102B TYR* 4.2 8.1 - - + +
213B LEU* 5.0 0.4 - - + -
216B ALA* 3.6 28.5 - - + -
218B LEU* 4.0 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A PHE* 5.8 4.7 - - + +
88B SER 3.1 9.6 + - - +
89B LYS* 4.6 2.7 - - - +
91B ILE* 1.3 77.7 - - - +
93B ASP* 1.3 62.8 + - - +
95B LYS* 3.0 27.8 + - + +
96B ASP* 2.7 48.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LYS* 2.9 32.1 + - - +
90B PHE* 3.6 6.8 - - - +
92B GLN* 1.3 79.1 - - - +
94B GLN* 1.3 62.8 + - - +
96B ASP* 3.1 24.2 + - - +
97B LYS* 3.1 29.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 2.9 50.8 + - + +
91B ILE* 3.2 10.5 - - - +
93B ASP* 1.3 77.6 - - - +
95B LYS* 1.3 60.1 + - - +
97B LYS* 3.3 24.4 + - - +
99B ILE* 3.1 67.0 + - + +
101B PRO* 5.1 9.2 - - + -
183B LYS* 4.3 18.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510A ASP* 3.4 25.6 + - - -
512A PHE* 3.4 32.5 - - - +
513A LYS* 6.0 0.4 - - - +
91B ILE* 2.9 31.7 + - - +
92B GLN* 3.0 34.1 + - + +
94B GLN* 1.3 77.2 - - - +
96B ASP* 1.3 59.1 + - - +
98B GLY* 3.2 17.5 + - - -
99B ILE 3.5 7.0 - - - -
100B ASN* 5.9 0.2 - - - -
101B PRO* 3.9 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLN* 2.7 43.8 + - - +
93B ASP* 3.1 19.4 + - - +
95B LYS* 1.3 77.8 - - - +
97B LYS* 1.3 58.7 + - + +
98B GLY 3.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP* 3.1 30.3 - - - +
94B GLN* 3.3 26.0 + - - +
95B LYS 3.1 0.6 - - - -
96B ASP* 1.3 79.5 - - + +
98B GLY* 1.3 58.1 + - - +
99B ILE* 3.2 19.9 + - + +
----------------------------------------------------------
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