Contacts of the helix formed by residues 70 - 88 (chain G) in PDB entry 3CJB
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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41G GLY 4.4 0.4 + - - -
68G GLU 3.5 3.3 + - - -
69G CYS* 1.3 77.5 - - - +
71G GLN* 1.3 60.4 + - - +
72G ASP* 2.6 23.6 + - - -
73G GLU* 2.8 24.1 + - - +
74G SER* 3.0 25.4 + - - -
123G SER* 3.5 19.7 - - - -
125G PHE* 5.7 1.1 - - - -
126G CA 3.9 2.5 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
144A ALA* 2.8 42.3 + - - +
334A GLU* 3.1 35.9 + - - +
341A ILE* 4.0 23.1 - - + +
345A ILE* 3.8 7.8 - - + +
70G SER* 1.3 71.2 - - - +
72G ASP* 1.3 60.4 + - - +
74G SER* 3.1 8.4 + - - +
75G GLY* 2.9 27.7 + - - -
125G PHE* 4.5 10.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 72 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ILE* 3.9 11.1 - - - +
22G VAL* 5.4 0.7 - - - +
24G LYS* 4.9 6.1 + - - -
25G PHE* 3.9 21.5 + - + -
70G SER* 2.6 28.4 + - - -
71G GLN* 1.3 75.5 - - - +
73G GLU* 1.3 65.5 + - - +
76G ALA* 3.0 29.6 + - - +
122G ALA 4.9 0.3 - - - +
123G SER* 2.8 20.6 + - - -
124G GLY* 2.9 22.2 + - - -
125G PHE* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 3.9 22.8 - - + +
23G GLU* 5.5 0.2 - - - -
24G LYS 5.6 2.4 + - - +
41G GLY 3.3 5.0 - - - +
42G ASP* 3.0 16.8 - - - +
43G ALA* 3.3 25.1 - - + +
69G CYS* 3.5 3.7 - - + +
70G SER* 2.8 33.8 + - - +
71G GLN 3.2 0.4 - - - -
72G ASP* 1.3 87.1 + - - +
74G SER* 1.3 60.1 + - - +
76G ALA* 3.7 0.9 - - - +
77G ALA 2.9 24.9 + - - -
121G VAL* 3.3 17.3 - - - +
122G ALA 4.0 4.1 - - - +
123G SER* 5.2 0.4 - - - -
126G CA 2.7 29.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A ALA 4.4 0.7 + - - -
145A SER 4.6 2.7 + - - -
146A GLY* 3.4 26.2 + - - -
43G ALA* 4.1 1.0 - - - +
65G LEU* 3.6 31.1 - - - +
69G CYS* 4.1 8.5 - - - -
70G SER 3.0 10.2 + - - -
71G GLN* 3.1 20.8 + - - +
73G GLU* 1.3 76.2 - - - +
75G GLY* 1.3 63.8 + - - +
77G ALA* 3.7 2.6 + - - +
78G ALA* 3.3 16.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 75 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.3 23.6 - - - +
144A ALA 5.2 0.2 - - - -
146A GLY* 4.2 0.4 - - - -
345A ILE* 4.3 15.3 - - - -
71G GLN 2.9 16.2 + - - -
72G ASP 4.2 0.7 - - - -
74G SER* 1.3 75.9 + - - +
76G ALA* 1.3 62.4 + - - +
78G ALA* 3.3 3.1 + - - +
79G ILE* 3.0 28.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
345A ILE* 4.0 5.0 - - + +
349A LEU* 4.1 16.6 - - + -
22G VAL* 3.5 26.2 - - + -
25G PHE* 5.1 4.0 - - + -
72G ASP 3.0 21.8 + - - +
73G GLU 3.4 0.6 + - - +
75G GLY* 1.3 73.2 - - - +
77G ALA* 1.3 56.2 + - - +
79G ILE* 3.2 3.4 + - - +
80G PHE* 2.8 53.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G VAL* 4.0 9.8 - - + +
43G ALA* 4.1 12.1 - - + -
44G TYR 4.0 19.7 - - - +
45G VAL* 4.1 5.9 - - - +
63G TYR* 4.0 13.4 - - + +
65G LEU* 4.5 3.4 - - + -
73G GLU 2.9 18.7 + - - +
74G SER 3.7 6.1 - - - +
76G ALA* 1.3 76.2 - - - +
78G ALA* 1.3 56.5 + - - +
80G PHE* 3.3 2.5 + - - +
81G THR* 2.9 34.4 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
143A TYR* 4.7 5.4 - - + +
146A GLY* 3.8 3.6 - - - -
147A ARG 3.7 28.9 - - - +
148A THR* 3.2 21.1 - - + +
63G TYR* 4.1 10.9 - - + -
74G SER 3.3 10.9 + - - +
75G GLY* 3.7 7.4 - - - +
76G ALA 3.3 0.6 - - - -
77G ALA* 1.3 77.0 - - - +
79G ILE* 1.3 64.1 + - - +
81G THR* 3.4 1.3 + - - +
82G VAL* 3.1 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.6 40.6 - - + -
342A GLY 4.7 2.0 - - - +
345A ILE* 4.6 8.1 - - + -
346A LEU* 3.8 43.3 - - + +
349A LEU* 3.3 26.7 - - + -
75G GLY 3.0 19.8 + - - +
76G ALA 3.8 3.4 - - - +
78G ALA* 1.3 71.7 - - - +
80G PHE* 1.3 60.4 + - - +
82G VAL* 3.1 9.2 + - + +
83G GLN* 2.8 42.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU* 3.3 24.9 - - + -
350A SER* 4.8 0.7 - - - -
351A THR* 3.5 33.9 - - + -
8G PHE* 4.8 2.5 - + - -
22G VAL* 4.3 6.3 - - + -
25G PHE 4.1 1.8 - - - -
26G ASP* 4.0 34.3 - - - -
27G LEU* 3.9 35.9 - - + -
45G VAL* 4.4 7.6 - - + -
76G ALA* 2.8 46.1 + - + +
77G ALA 3.7 5.2 - - - +
79G ILE* 1.3 72.6 - - - +
81G THR* 1.3 58.2 + - - +
83G GLN* 3.2 13.8 + - - +
84G LEU* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.7 0.4 - - - -
45G VAL* 4.2 11.4 - - - +
61G LEU* 3.6 33.4 - - + +
62G HIS 4.9 0.2 - - - -
63G TYR* 3.3 37.4 + - + +
77G ALA 2.9 17.3 + - - -
78G ALA 3.7 5.2 - - - -
80G PHE* 1.3 76.5 - - - +
82G VAL* 1.3 61.7 + - - +
84G LEU* 4.6 0.2 - - - -
85G ASP* 3.2 23.7 + - - +
94G GLN* 3.8 22.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A TYR* 3.7 26.5 - - + +
148A THR* 3.5 18.6 - - + -
167A GLU 4.1 4.9 - - - +
168A GLY* 3.7 27.4 - - - -
169A TYR* 4.3 9.2 - - + -
78G ALA 3.1 16.0 + - - +
79G ILE* 3.1 9.5 + - + +
81G THR* 1.3 76.8 - - - +
83G GLN* 1.3 62.0 + - + +
85G ASP* 3.8 2.9 + - - +
86G ASP* 3.2 31.4 + - - +
94G GLN* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.7 1.0 - - - +
349A LEU* 4.1 3.8 - - - +
351A THR* 2.5 41.9 + - - +
352A PHE* 4.7 7.1 - - - +
355A MET* 4.3 31.5 - - + +
3G VAL* 5.2 9.0 - - + +
8G PHE* 4.0 12.2 - - + -
79G ILE* 2.8 37.2 + - + +
80G PHE* 3.2 11.6 + - - +
82G VAL* 1.3 76.9 - - + +
84G LEU* 1.3 59.9 + - - +
85G ASP 3.2 1.6 - - - -
86G ASP* 3.3 7.7 + - - +
87G TYR* 2.9 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G GLU 6.0 0.2 - - - -
8G PHE* 3.1 48.9 - - + -
11G ALA* 3.6 31.2 - - + -
20G TRP* 5.5 7.0 - - + -
27G LEU* 4.0 18.4 - - + -
45G VAL* 5.4 4.7 - - + -
47G LEU* 5.1 4.0 - - + -
61G LEU* 3.3 29.4 - - + -
80G PHE* 2.8 26.1 + - + +
83G GLN* 1.3 72.1 - - - +
85G ASP* 1.3 57.2 + - - +
87G TYR* 3.3 2.6 + - + +
88G LEU* 2.9 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A GLU* 3.6 13.0 - - - +
61G LEU* 3.8 6.0 - - + +
81G THR 3.2 16.8 + - - +
82G VAL 3.8 3.4 - - - +
83G GLN 3.2 0.6 - - - -
84G LEU* 1.3 78.3 - - - +
86G ASP* 1.3 60.1 + - - +
88G LEU* 3.1 10.9 + - - +
90G GLY* 2.7 42.3 + - - +
92G ALA* 2.8 46.1 + - - +
94G GLN* 3.5 24.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TYR* 2.5 43.2 + - - -
1G MET* 4.5 28.7 - - + +
82G VAL* 3.2 17.8 + - - +
83G GLN* 3.3 9.8 + - - +
85G ASP* 1.3 82.8 - - - +
87G TYR* 1.3 63.8 + - - +
89G ASN* 3.0 17.2 + - - -
90G GLY* 3.9 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1G MET* 4.9 11.4 - - + +
2G VAL* 5.8 4.7 - - + -
3G VAL* 4.0 33.4 - - + -
8G PHE* 3.0 54.6 + + + -
9G LEU* 3.3 29.1 - - + +
11G ALA 5.1 0.9 - - - -
83G GLN 2.9 16.5 + - - +
84G LEU* 3.5 7.0 - - + +
85G ASP 3.3 0.2 - - - -
86G ASP* 1.3 77.4 - - - +
88G LEU* 1.3 76.9 + - + +
89G ASN* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G ALA* 4.2 15.0 - - + +
47G LEU* 4.2 17.5 - - + -
59G TYR* 3.9 50.2 - - + +
61G LEU* 5.6 1.3 - - + -
84G LEU* 2.9 28.7 + - + +
85G ASP* 3.1 6.2 + - - +
87G TYR* 1.3 100.0 - - + +
89G ASN* 1.3 72.8 + - - +
91G ARG* 3.3 22.6 + - - +
92G ALA* 5.2 6.3 - - + +
----------------------------------------------------------
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