Contacts of the helix formed by residues 66 - 77 (chain G) in PDB entry 1IB1
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 66 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49G PHE* 4.0 13.9 - - + -
63G CYS* 4.4 4.0 + - - -
65G LEU* 1.3 74.5 - - - +
67G LEU* 1.3 66.8 + - - +
68G ASP* 3.0 22.7 + - - +
69G GLU* 2.8 52.0 + - - +
70G VAL* 2.9 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ALA* 3.9 5.2 - - + +
46G ALA* 3.5 38.1 - - + +
49G PHE* 3.7 28.2 - - + -
66G ASN* 1.3 72.4 - - - +
68G ASP* 1.3 58.0 + - - +
70G VAL* 3.1 8.5 + - - +
71G GLN* 2.8 63.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 68 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66G ASN* 3.0 11.6 + - - +
67G LEU* 1.3 77.6 - - - +
69G GLU* 1.3 68.0 + - - +
71G GLN* 3.2 13.7 + - - +
72G HIS* 2.8 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G CYS 5.5 0.2 - - - +
64G PRO 3.9 5.0 - - - +
65G LEU* 3.4 28.9 - - + +
66G ASN* 2.8 52.2 + - - +
68G ASP* 1.3 80.8 - - - +
70G VAL* 1.3 60.3 + - - +
72G HIS* 3.4 9.0 + - - +
73G PHE* 3.2 28.6 + - + -
109G LEU* 5.2 5.4 - - - +
110G ALA* 4.8 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 70 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45G ALA* 3.9 23.1 - - + +
48G VAL* 3.8 24.7 - - + -
49G PHE 5.3 0.7 - - - +
52G GLU* 3.8 11.0 - - - +
65G LEU* 3.4 37.2 - - + +
66G ASN 2.9 18.3 + - - +
67G LEU* 3.4 9.4 - - - +
69G GLU* 1.3 72.5 - - - +
71G GLN* 1.3 66.1 + - - +
73G PHE* 3.4 4.5 + - - +
74G LEU* 3.1 31.0 + - + +
95G ILE* 4.4 8.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 71 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G PRO* 4.0 15.0 + - + +
45G ALA* 3.2 25.1 - - + +
67G LEU* 2.8 39.9 + - - +
68G ASP* 3.5 11.4 - - - +
70G VAL* 1.3 76.5 - - - +
72G HIS* 1.3 63.2 + - - +
74G LEU* 3.2 5.4 + - - +
75G THR* 2.8 31.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASP* 2.8 16.1 + - - +
69G GLU* 3.4 13.9 + - - +
71G GLN* 1.3 78.4 - - - +
73G PHE* 1.3 75.0 + + - +
75G THR* 3.7 4.7 - - - -
76G LEU* 2.9 63.1 + - + +
110G ALA* 4.1 20.2 + - + +
112G HIS* 5.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G LEU* 3.8 15.0 - - + -
69G GLU* 3.2 14.2 + - + -
70G VAL 3.4 2.2 + - - +
72G HIS* 1.3 98.2 - + - +
74G LEU* 1.3 59.0 + - - +
76G LEU* 4.5 1.3 - - + -
77G CYS* 2.8 40.8 + - - +
95G ILE* 3.8 27.6 - - + -
96G GLY 4.1 7.9 - - - +
97G SER* 3.6 22.2 - - - -
109G LEU 3.5 14.6 - - - -
110G ALA* 3.9 13.5 - - - -
111G LEU 4.0 11.0 - - - -
112G HIS* 4.2 5.6 - - + -
122G HIS* 3.4 40.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40G LEU* 3.7 24.7 - - + +
41G THR 3.1 22.7 - - - +
42G PRO* 3.7 24.3 - - + +
44G ASP 4.6 1.1 - - - +
45G ALA* 4.2 15.9 - - + +
48G VAL* 5.1 0.4 - - + -
70G VAL* 3.1 27.5 + - + +
71G GLN 3.2 4.2 + - - +
73G PHE* 1.3 78.3 - - - +
75G THR* 1.3 57.2 + - - +
78G PRO* 3.2 26.6 - - + +
81G SER* 3.4 35.9 - - - +
95G ILE* 3.9 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G PRO* 3.6 22.7 - - + +
71G GLN* 2.8 23.2 + - - +
72G HIS* 3.7 5.1 - - - -
74G LEU* 1.3 75.8 - - - +
76G LEU* 1.3 66.1 + - - +
78G PRO* 3.8 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G HIS* 2.9 49.1 + - + +
73G PHE* 4.2 2.9 - - + +
75G THR* 1.3 81.0 - - - +
77G CYS* 1.3 61.6 + - - +
78G PRO* 3.7 3.0 - - - +
79G GLU* 4.6 2.1 - - - +
112G HIS* 3.8 40.3 + - + +
114G PRO* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G PHE* 2.8 30.9 + - - +
76G LEU* 1.3 77.0 - - - +
78G PRO* 1.3 59.8 - - - +
79G GLU* 3.1 22.2 - - - +
80G LEU* 3.0 29.7 + - + +
81G SER* 4.1 1.2 + - - -
96G GLY 3.6 20.3 - - - +
97G SER* 3.8 10.1 - - - -
112G HIS* 3.8 34.5 - - - +
----------------------------------------------------------
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