Contacts of the helix formed by residues 72 - 86 (chain G) in PDB entry 2QJK
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 HIS 72 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G THR* 2.9 14.4 + - + -
71G PRO* 1.3 78.5 - - - +
73G VAL* 1.3 59.6 + - + +
74G ASP* 2.8 41.9 + - + +
75G LEU* 2.6 33.8 + - + -
76G ALA 3.0 8.9 + - - -
188G ASN* 3.3 27.4 + - - +
191G LEU* 3.8 7.0 - - - +
70J THR* 4.1 21.3 - - + +
75J LEU* 4.0 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G HIS* 1.3 79.2 - - + +
74G ASP* 1.3 81.5 + - - +
75G LEU 3.2 1.9 + - - -
76G ALA* 4.1 6.2 + - - +
77G PHE* 4.7 3.5 + - - +
151G TRP* 3.7 48.7 - - + +
187G ASP* 4.4 6.5 - - - +
188G ASN* 2.9 43.2 + - + +
191G LEU* 3.4 13.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G HIS* 2.8 30.1 + - + -
73G VAL* 1.3 87.8 - - - +
75G LEU* 1.3 71.3 + - + +
78G ALA* 4.9 4.7 + - - +
75J LEU* 6.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G THR* 3.5 33.7 - - + -
72G HIS* 2.6 13.4 + - - +
73G VAL 4.2 0.2 - - - -
74G ASP* 1.3 86.7 - - + +
76G ALA* 1.3 67.2 + - - +
77G PHE 3.2 1.8 - - - -
78G ALA* 2.7 25.7 + - + +
79G SER* 2.8 10.9 + - - +
72J HIS* 3.9 26.5 - - + +
75J LEU* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 3.8 19.5 - - - +
70G THR 3.0 22.8 + - - +
72G HIS 3.0 19.9 + - - +
73G VAL 4.3 2.7 - - - +
75G LEU* 1.3 73.7 - - - +
77G PHE* 1.3 60.1 + - - +
79G SER* 2.8 21.1 + - - -
80G VAL* 3.1 13.9 + - - +
149G LEU 3.9 8.1 - - - +
150G PRO 4.3 1.8 - - - -
151G TRP* 4.1 6.5 - - + -
191G LEU* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G VAL 4.7 4.5 + - - +
75G LEU 2.8 4.6 + - - -
76G ALA* 1.3 72.8 - - - +
78G ALA* 1.3 65.3 + - - +
80G VAL* 2.8 19.0 + - + +
81G GLU* 3.1 16.8 + - + +
94G ARG* 6.0 3.1 - - - -
150G PRO* 3.1 31.4 + - + +
151G TRP* 4.0 15.2 - - + +
152G GLY* 4.6 0.7 - - - -
279G ASN 3.7 20.6 - - - -
280G TYR* 3.8 27.8 - + - -
281G ILE 4.6 3.6 - - - -
282G GLU* 3.2 36.1 - - + +
44H PHE* 3.5 30.5 - + - -
102H LEU* 4.2 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 78 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74G ASP 4.9 3.6 - - - +
75G LEU* 2.7 18.7 + - + +
77G PHE* 1.3 74.4 - - - +
79G SER* 1.3 65.8 + - - +
81G GLU* 2.8 3.6 + - - +
82G HIS* 2.7 26.1 + - - +
44H PHE* 3.9 30.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G HIS 3.5 4.3 + - - +
69G TYR* 3.1 14.7 - - - -
70G THR* 2.7 37.6 + - - -
75G LEU* 2.8 11.9 + - - -
76G ALA* 2.8 23.4 + - - -
78G ALA* 1.3 76.1 - - - +
80G VAL* 1.3 59.0 + - - -
82G HIS* 3.1 23.0 - - - +
83G ILE* 3.2 13.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G TYR* 3.9 23.8 - - + -
76G ALA 3.1 12.1 + - - +
77G PHE* 2.8 12.5 + - + +
79G SER* 1.3 73.5 - - - +
81G GLU* 1.3 66.7 + - - +
82G HIS 3.0 1.6 - - - -
83G ILE* 3.1 11.0 + - + +
84G MET* 3.0 20.2 + - + +
94G ARG* 3.7 32.5 - - + +
150G PRO* 4.1 14.6 - - + +
502G HEM 3.5 30.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PHE* 3.1 17.1 + - + +
78G ALA 2.8 10.3 + - - +
80G VAL* 1.3 74.6 - - + +
82G HIS* 1.3 64.0 + - - +
84G MET* 2.9 21.9 + - - +
85G ARG* 2.7 71.6 + - - +
94G ARG* 4.9 1.2 + - - -
280G TYR* 4.6 7.6 - - - -
44H PHE* 4.3 30.7 - - + -
102H LEU* 3.3 32.9 - - + +
105H LYS* 4.6 4.3 + - - -
219H ALA 4.5 3.5 - - - +
221H PRO* 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G HIS* 4.6 13.5 + - + -
78G ALA 2.7 12.4 + - - +
79G SER* 3.1 16.2 - - - +
81G GLU* 1.3 77.7 - - - +
83G ILE* 1.3 61.6 + - + +
85G ARG* 5.0 2.0 - - - +
86G ASN* 2.6 73.0 + - + +
87G VAL* 4.0 20.8 - - + +
41I SER* 4.5 5.6 + - - -
43I ASP* 3.6 26.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G LEU* 3.6 41.7 - - + +
68G HIS* 3.6 37.5 - - + +
69G TYR* 4.2 7.0 - - + +
79G SER 3.3 14.1 - - - +
80G VAL* 3.1 18.1 + - + +
82G HIS* 1.3 76.9 - - + +
84G MET* 1.3 63.5 + - - +
87G VAL* 3.6 21.7 + - + +
90G GLY* 3.1 36.8 - - - +
93G LEU* 6.2 0.4 - - + -
94G ARG* 4.8 5.6 - - + -
502G HEM 5.3 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G VAL* 3.0 18.2 + - + +
81G GLU* 2.9 29.0 + - - +
83G ILE* 1.3 78.4 - - - +
85G ARG* 1.3 60.9 + - + +
87G VAL 4.9 1.6 - - - +
91G PHE* 3.5 37.0 + - + +
94G ARG* 3.4 50.5 - - + +
95G TYR* 3.5 40.6 - - + +
105H LYS* 3.7 13.7 - - - +
220H GLU* 5.0 3.4 - - - +
221H PRO* 5.9 1.1 - - - -
222H LYS* 4.0 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G GLU* 2.7 48.9 + - - +
82G HIS* 4.1 1.1 - - - +
84G MET* 1.3 76.4 - - + +
86G ASN* 1.3 73.2 + - - +
87G VAL 5.1 0.4 - - - -
44H PHE* 2.9 35.5 + - - +
45H VAL* 3.9 16.9 - - - +
46H PRO* 4.2 13.4 - - + +
49H SER* 5.4 2.2 + - - -
52H GLU* 4.9 2.4 - - - +
88H HIS* 6.0 0.7 - - - -
101H SER* 3.9 9.1 + - - -
102H LEU* 5.0 1.0 - - - +
218H ALA 2.9 29.3 + - - -
219H ALA* 3.9 11.7 + - - +
221H PRO* 3.7 26.5 - - + +
222H LYS* 3.8 26.1 + - - +
42I ALA* 4.6 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G HIS* 2.6 54.8 + - + +
84G MET 3.6 0.6 - - - -
85G ARG* 1.3 88.7 - - - +
87G VAL* 1.3 69.8 + - - +
88G ASN* 3.3 4.7 + - - +
46H PRO* 4.8 3.8 - - - +
48H ARG* 3.1 30.0 + - - +
52H GLU* 5.3 0.2 - - - +
88H HIS* 5.7 6.7 - - - -
41I SER* 4.0 2.8 - - - -
42I ALA* 3.6 24.2 + - - +
43I ASP* 4.0 16.6 - - - +
----------------------------------------------------------
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