Contacts of the helix formed by residues 70 - 87 (chain B) in PDB entry 1C3Q
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 SER 70 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR 5.0 2.0 - - - -
69B LEU* 1.3 73.6 - - - +
71B LYS* 1.3 65.7 + - - +
72B GLU* 3.5 8.4 + - - +
73B SER* 3.0 38.7 + - - -
74B VAL* 3.1 10.0 + - - +
103B PHE* 4.0 5.8 - - - -
48C ALA* 4.3 12.3 - - - -
50C GLU* 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B SER* 1.3 73.1 - - - +
72B GLU* 1.3 69.3 + - - +
74B VAL* 3.4 5.7 + - - +
75B GLU* 2.9 61.3 + - + +
103B PHE* 3.8 17.7 - - + -
49C LYS* 6.5 0.4 - - - +
50C GLU* 4.3 25.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A SER* 6.1 1.0 - - - -
49B LYS* 3.9 18.4 - - + +
70B SER* 3.1 7.5 + - - +
71B LYS* 1.3 88.3 + - - +
73B SER* 1.3 60.8 + - - +
75B GLU* 3.3 12.9 + - - +
76B ALA* 3.1 21.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.5 6.3 - - - +
47B TYR* 5.8 4.0 - - - -
68B THR 5.5 2.0 - - - -
69B LEU* 3.6 10.4 - - - +
70B SER* 3.0 40.2 + - - -
72B GLU* 1.3 74.6 - - - +
74B VAL* 1.3 59.8 + - - +
76B ALA* 3.2 8.7 + - - +
77B MET* 2.8 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ILE* 5.1 1.1 - - + -
69B LEU* 3.9 21.1 - - + -
70B SER 3.1 15.8 + - - +
71B LYS* 3.7 7.9 - - - +
73B SER* 1.3 73.8 + - - +
75B GLU* 1.3 69.6 + - + +
77B MET* 3.1 14.2 + - - +
78B ILE* 3.1 37.0 + - + +
103B PHE* 4.9 1.6 - - + -
107B SER* 3.9 39.7 - - - +
110B ASP* 5.1 5.2 - - + +
111B ILE* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 2.6 39.6 + - - +
71B LYS* 2.9 51.1 + - + +
72B GLU* 3.6 5.7 - - - +
74B VAL* 1.3 78.2 - - + +
76B ALA* 1.3 61.9 + - - +
78B ILE* 3.3 10.9 + - - +
79B ILE* 3.1 29.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 4.5 5.4 - - + -
47B TYR* 3.3 27.6 - - + +
49B LYS* 4.3 17.4 - - + +
52B VAL* 3.7 9.8 - - + +
72B GLU* 3.1 13.5 + - + +
73B SER* 3.4 12.6 - - - +
74B VAL 3.2 0.2 - - - -
75B GLU* 1.3 78.3 - - - +
77B MET* 1.3 56.3 + - - +
79B ILE* 3.3 6.0 + - - +
80B ALA* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B ILE* 3.6 38.1 - - + +
24B THR* 5.2 1.6 - - - +
64B LEU* 3.8 32.1 - - + +
65B ASN 3.2 28.7 - - - +
66B ILE* 3.9 15.7 - - + -
69B LEU* 5.1 3.4 - - + -
73B SER* 2.8 37.3 + - - +
74B VAL* 3.1 13.2 + - - +
76B ALA* 1.3 76.7 - - - +
78B ILE* 1.3 56.4 + - - +
80B ALA* 3.4 2.3 + - - +
81B GLY* 2.8 26.0 + - - -
111B ILE* 3.9 24.7 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
74B VAL* 3.1 27.4 + - + +
75B GLU* 3.7 9.2 - - - +
77B MET* 1.3 75.5 - - - +
79B ILE* 1.3 67.5 + - + +
81B GLY 3.3 0.2 + - - -
82B LYS* 2.9 42.4 + - + +
110B ASP* 4.2 26.0 - - + +
111B ILE* 4.2 18.6 - - + -
114B GLU* 3.6 29.6 - - + -
115B VAL* 4.1 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B LYS* 4.0 42.2 - - + +
52B VAL* 3.7 15.5 - - + -
53B ALA* 4.2 16.1 - - + +
75B GLU* 3.1 20.9 + - + +
76B ALA* 3.6 7.0 - - - +
78B ILE* 1.3 77.7 - - + +
80B ALA* 1.3 62.7 + - - +
82B LYS* 3.5 7.6 + - - +
83B SER* 3.2 21.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B HIS* 4.8 0.2 - - + -
23B ILE* 3.5 26.0 - - + -
52B VAL* 3.9 26.9 - - + +
56B ALA* 3.6 3.1 - - + +
62B LEU* 3.5 19.3 - - + +
76B ALA 2.9 17.0 + - - +
77B MET 3.6 2.2 - - - +
79B ILE* 1.3 76.5 - - - +
81B GLY* 1.3 65.6 + - - +
83B SER* 3.2 4.6 + - - -
84B ALA* 2.9 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LEU* 3.6 14.5 - - - +
64B LEU* 4.8 0.7 - - - -
77B MET 2.8 19.6 + - - -
78B ILE 3.3 1.7 + - - -
80B ALA* 1.3 73.4 - - - +
82B LYS* 1.3 56.8 + - - +
84B ALA* 3.2 3.9 + - - +
85B ASN* 2.8 32.7 + - - +
91B VAL* 4.4 1.8 - - - -
115B VAL* 3.7 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 2.9 35.6 + - + +
79B ILE* 3.8 6.3 - - - +
81B GLY* 1.3 72.4 - - - +
83B SER* 1.3 64.8 + - - +
85B ASN* 3.4 10.6 + - - +
86B GLU* 3.1 23.6 + - - +
114B GLU* 3.0 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B ALA* 2.7 46.4 + - - +
56B ALA* 4.4 1.8 - - - -
57B LYS* 3.8 12.1 + - - +
79B ILE 3.2 8.6 + - - -
80B ALA 3.2 9.7 + - - -
82B LYS* 1.3 73.2 - - - +
84B ALA* 1.3 67.0 + - - +
86B GLU* 3.3 4.4 + - - -
87B HIS* 2.8 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B ALA* 4.4 7.7 - - + +
62B LEU* 3.8 9.2 - - + -
80B ALA 2.9 13.4 + - - +
81B GLY 3.4 9.0 - - - +
83B SER* 1.3 77.1 - - - +
85B ASN* 1.3 61.2 + - - +
87B HIS* 3.1 1.8 + - - -
88B GLY 3.0 5.4 + - - -
89B VAL* 2.8 50.7 + - + +
91B VAL* 3.4 23.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLY 2.8 18.5 + - - +
82B LYS* 3.6 10.0 - - - +
84B ALA* 1.3 75.8 - - - +
86B GLU* 1.3 62.0 + - - +
87B HIS 3.2 1.2 + - - -
88B GLY* 3.3 11.5 + - - -
89B VAL 4.8 2.4 - - - +
91B VAL* 3.8 8.1 - - - +
114B GLU 4.3 2.8 + - - -
115B VAL* 3.5 12.8 - - - +
116B ARG* 2.9 82.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
82B LYS 3.1 13.1 + - - +
83B SER* 3.3 6.3 + - - +
85B ASN* 1.3 78.3 - - - +
87B HIS* 1.3 71.9 + - + +
88B GLY 3.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B LYS* 3.6 49.8 + - + +
83B SER* 2.8 30.5 + - - +
84B ALA 3.1 3.8 + - - +
85B ASN 3.1 0.8 - - - -
86B GLU* 1.3 91.3 - - + +
88B GLY* 1.3 63.2 + - - +
89B VAL* 3.3 13.0 + - + +
----------------------------------------------------------
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