Contacts of the helix formed by residues 74 - 89 (chain B) in PDB entry 3FWQ
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 LYS 74 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B VAL* 1.3 98.0 - - + +
75B LYS* 1.3 60.2 + - - +
76B LYS* 4.0 29.4 - - + +
77B LYS* 3.0 39.3 + - + +
78B ILE* 3.1 9.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B VAL* 5.2 0.4 - - - -
33B TRP* 3.9 36.7 - - + +
73B VAL 3.6 1.8 + - - -
74B LYS* 1.3 72.6 - - - +
76B LYS* 1.3 55.6 + - - +
77B LYS 3.3 0.2 - - - -
78B ILE* 3.5 21.8 + - + +
79B LYS* 3.0 51.4 + - + +
102B LYS* 4.6 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.2 29.4 - - + +
27B GLU* 5.1 14.4 - - + +
74B LYS* 3.1 29.9 + - + +
75B LYS* 1.3 78.3 - - - +
77B LYS* 1.3 80.3 + - + +
79B LYS* 3.7 7.5 + - - +
80B ARG 3.0 19.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 5.7 2.9 - - - +
73B VAL* 4.2 17.3 - - + -
74B LYS* 3.0 35.1 + - + +
76B LYS* 1.3 98.3 - - + +
78B ILE* 1.3 61.2 + - - +
80B ARG* 3.4 45.8 + - - +
81B GLU* 3.0 28.4 + - - +
177B GLY 5.5 1.7 - - - +
189B ASN* 5.7 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B TRP* 4.1 9.4 - - + -
70B LEU* 4.7 9.6 - - + +
71B LYS 6.0 0.4 - - - +
73B VAL* 3.4 35.0 - - + +
74B LYS 3.1 7.5 + - - +
75B LYS* 3.5 26.0 - - + +
76B LYS 3.4 0.2 - - - -
77B LYS* 1.3 77.4 - - - +
79B LYS* 1.3 58.3 + - + +
81B GLU* 3.3 8.2 + - - +
82B ILE* 2.9 52.7 + - + +
109B PRO* 3.6 40.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
26B TYR* 3.7 21.3 - - - +
27B GLU* 4.1 13.7 + - - +
28B SER 5.4 0.2 - - - -
29B HIS* 3.0 33.9 + - - +
30B VAL* 4.5 6.7 - - - +
31B VAL* 3.6 29.6 - - + +
75B LYS* 3.0 44.0 + - + +
76B LYS* 3.8 8.3 - - - +
78B ILE* 1.3 71.9 - - + +
80B ARG* 1.3 58.5 + - - +
82B ILE* 3.8 6.0 - - - +
83B LYS* 2.7 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TYR* 3.5 36.2 + - + -
76B LYS 3.0 17.3 + - - +
77B LYS* 3.4 47.2 + - - +
78B ILE 3.3 0.2 - - - -
79B LYS* 1.3 75.6 - - - +
81B GLU* 1.3 57.9 + - - +
83B LYS* 4.0 1.0 - - - +
84B ILE* 3.0 46.6 + - + +
155B ARG* 3.2 26.4 - - - +
177B GLY 3.5 20.6 + - - -
178B LEU* 3.7 7.3 + - - +
179B ALA 3.0 18.4 + - - -
180B GLU* 2.8 32.1 + - - +
181B PHE* 4.7 0.2 - - - -
189B ASN* 6.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 5.6 0.2 - - - -
68B LYS* 3.6 15.8 + - - -
70B LEU* 3.4 21.3 - - - +
77B LYS 3.0 16.4 + - - +
78B ILE* 3.7 6.3 - - - +
80B ARG* 1.3 74.1 - - - +
82B ILE* 1.3 61.3 + - + +
84B ILE* 3.4 4.6 + - - +
85B LEU* 2.9 43.6 + - + +
111B LEU* 3.2 28.9 - - - +
176B TRP 3.5 25.2 + - - +
177B GLY* 3.6 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B HIS* 4.6 10.5 - - + +
31B VAL* 3.9 25.6 - - + -
33B TRP* 4.3 1.3 - - + -
70B LEU* 5.9 0.2 - - + -
78B ILE* 2.9 40.6 + - + +
79B LYS* 3.8 4.0 - - - +
81B GLU* 1.3 76.7 - - - +
83B LYS* 1.3 57.1 + - - +
85B LEU* 3.2 7.8 + - - +
86B GLU* 2.8 41.8 + - - +
97B LEU* 4.3 6.5 - - + +
100B ILE* 3.8 41.3 - - + -
111B LEU* 4.2 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLU* 3.0 33.3 + - - +
23B TYR* 3.4 20.8 - - - +
26B TYR* 4.0 20.4 - - + -
29B HIS* 3.7 35.1 - - + +
79B LYS 2.7 21.6 + - - +
80B ARG 4.1 0.9 - - - +
82B ILE* 1.3 71.1 - - - +
84B ILE* 1.3 59.5 + - - +
86B GLU* 3.2 31.6 + - - +
87B ASN* 2.9 44.9 + - - +
181B PHE* 4.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ARG* 3.0 31.6 + - + +
81B GLU* 3.7 6.5 - - - +
83B LYS* 1.3 76.1 - - - +
85B LEU* 1.3 63.3 + - - +
87B ASN* 3.2 11.3 + - - +
88B LEU* 3.2 24.7 + - + +
152B ILE* 3.8 32.3 - - + -
176B TRP* 4.1 8.7 - - + -
179B ALA* 3.5 44.6 - - + +
180B GLU* 3.7 13.0 - - - +
181B PHE* 3.6 22.2 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
81B GLU* 2.9 29.9 + - + +
82B ILE 3.6 3.8 - - - +
84B ILE* 1.3 77.6 - - - +
86B GLU* 1.3 60.1 + - - +
88B LEU* 3.3 13.4 + - + +
89B ARG* 3.3 14.4 + - - +
94B ILE* 5.4 2.8 - - + +
95B ILE* 4.4 14.6 - - + +
97B LEU* 4.0 22.2 + - + +
111B LEU* 3.8 23.1 - - + -
113B PHE* 3.7 38.4 - - + -
176B TRP* 3.7 39.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 5.7 1.4 + - - -
29B HIS* 3.3 30.8 + - - -
82B ILE* 2.8 25.6 + - - +
83B LYS* 3.2 42.3 + - + +
85B LEU* 1.3 70.1 - - - +
87B ASN* 1.3 65.7 + - - +
88B LEU 3.2 0.4 - - - -
89B ARG* 3.3 41.5 - - - +
97B LEU* 4.6 4.0 - - + +
100B ILE* 5.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 4.3 15.5 + - - -
23B TYR* 3.2 59.9 + - + +
83B LYS* 2.9 28.8 + - - +
84B ILE 3.2 6.3 + - - +
86B GLU* 1.3 79.1 - - - +
88B LEU* 1.3 62.0 + - - +
89B ARG 3.6 0.4 - - - -
146B TYR* 4.6 5.2 + - - -
150B MET* 4.7 8.3 - - - +
152B ILE* 4.2 6.3 - - + -
181B PHE* 3.3 26.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ILE* 3.2 29.7 + - + +
85B LEU* 3.3 6.7 + - - +
86B GLU 3.2 0.4 - - - -
87B ASN* 1.3 76.9 - - - +
89B ARG* 1.3 61.0 + - - +
91B GLY* 2.8 27.1 + - - -
94B ILE* 4.2 19.9 - - + +
95B ILE 5.9 0.4 - - - -
146B TYR* 4.1 10.8 - - + -
147B CYS* 3.7 28.3 - - + -
150B MET* 3.8 23.6 - - + -
152B ILE* 3.8 9.0 - - + -
176B TRP* 3.7 41.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLU* 4.8 21.0 + - - +
114A GLU* 5.8 9.6 - - - +
170A LYS* 4.2 16.2 + - - +
172A ARG* 4.7 3.1 + - - -
85B LEU 3.3 8.5 + - - +
86B GLU* 3.3 33.8 - - - +
87B ASN 4.7 0.3 - - - +
88B LEU* 1.3 77.7 - - - +
90B GLY* 1.3 60.5 + - - +
94B ILE 6.2 0.2 - - - -
95B ILE 5.5 1.1 - - - -
96B THR* 4.1 25.8 - - + +
97B LEU* 2.9 48.1 + - - +
98B ALA 4.7 5.3 + - - -
99B ASP* 5.0 1.2 - - - +
100B ILE* 5.6 4.0 - - - +
146B TYR* 4.7 1.7 + - - -
----------------------------------------------------------
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