Contacts of the helix formed by residues 77 - 95 (chain G) in PDB entry 2JG7
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 PRO 77 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E SER 3.3 21.5 - - - +
143E GLU* 3.4 26.7 - - - +
144E ARG 3.9 1.6 - - - +
145E PRO* 3.7 31.4 - - + -
75G ASP 3.4 9.4 - - - +
76G ILE* 1.3 92.0 - - + +
78G ALA* 1.3 65.5 + - - +
79G PRO* 4.1 0.7 - - + -
80G LYS* 3.0 15.0 + - + +
81G ARG* 3.0 18.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
141E PRO* 3.8 16.9 - - + +
142E SER 4.4 1.4 + - - -
76G ILE 3.6 1.2 + - - -
77G PRO* 1.3 71.0 - - - +
79G PRO* 1.4 64.5 - - + +
81G ARG* 3.0 35.8 + - - +
82G GLY 2.9 23.6 + - - -
132G SER* 3.2 23.5 - - - +
135G ILE* 4.2 10.1 - - + -
181G THR 4.0 6.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 79 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E PRO* 3.7 15.9 - - + +
142E SER 3.6 13.0 - - - +
143E GLU* 3.8 16.4 - - + +
77G PRO 3.5 4.0 - - - -
78G ALA* 1.4 90.8 - - + +
80G LYS* 1.3 56.3 + - - +
82G GLY* 3.3 2.6 + - - -
83G GLU* 3.1 22.7 + - - +
132G SER* 3.4 25.2 + - - +
133G ARG* 3.5 43.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 80 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143E GLU* 3.1 38.5 + - + +
145E PRO* 5.4 6.4 - - + +
76G ILE* 3.7 15.7 - - + +
77G PRO* 3.0 22.8 + - + +
79G PRO* 1.3 77.9 - - - +
81G ARG* 1.3 63.6 + - - +
83G GLU* 3.4 21.4 - - + +
84G ILE* 3.5 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 81 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TRP* 3.6 38.6 + - + -
74G ALA 4.0 12.7 + - - -
76G ILE* 2.9 29.7 + - + +
77G PRO* 3.0 15.6 + - - +
78G ALA* 3.3 28.8 - - - +
80G LYS* 1.3 74.6 - - - +
82G GLY* 1.3 58.3 + - - +
84G ILE* 3.1 7.7 + - - +
85G VAL* 3.0 28.8 + - - +
135G ILE* 4.7 1.8 - - - +
155G PRO* 4.5 7.9 - - - +
180G LEU 3.2 19.7 - - - +
181G THR* 2.6 33.2 + - - +
182G CYS* 3.4 4.6 + - - +
183G GLY* 3.1 27.6 - - - +
488G MET* 5.6 1.6 - - - +
444H PRO* 6.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 82 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78G ALA 2.9 12.8 + - - -
79G PRO 3.3 5.6 + - - -
80G LYS 3.3 0.2 - - - -
81G ARG* 1.3 75.1 - - - +
83G GLU* 1.3 53.1 + - - +
85G VAL* 3.2 9.4 + - - -
86G ARG* 2.7 35.0 + - - +
129G VAL* 3.5 16.4 - - - +
132G SER* 3.8 18.4 - - - -
181G THR* 4.8 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93F ARG* 5.1 1.8 + - - -
123F ASP* 5.6 1.9 - - - +
126F ASP* 5.4 0.2 - - - +
79G PRO 3.1 11.8 + - - +
80G LYS* 3.4 16.2 - - + +
81G ARG 3.2 0.4 - - - -
82G GLY* 1.3 74.7 - - - +
84G ILE* 1.3 67.9 + - + +
86G ARG* 2.5 44.1 + - - +
87G GLN* 2.9 41.4 + - - +
129G VAL* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 84 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G TRP* 4.0 18.4 - - + -
76G ILE* 6.3 0.9 - - + -
80G LYS 3.7 13.9 - - - +
81G ARG 3.1 8.2 + - - +
83G GLU* 1.3 79.0 - - + +
85G VAL* 1.3 67.0 + - - +
87G GLN* 3.0 17.8 + - - +
88G ILE* 3.0 23.6 + - + +
180G LEU* 5.3 3.1 - - + -
208G VAL* 4.2 7.6 - - + +
209G LEU* 4.1 25.8 - - + -
212G ASN* 3.6 29.2 - - + +
214G LEU* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 85 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81G ARG 3.0 13.4 + - - +
82G GLY* 3.6 9.4 - - - +
84G ILE* 1.3 74.6 - - + +
86G ARG* 1.3 61.9 + - - +
88G ILE* 3.2 10.8 + - + +
89G GLY 3.0 18.5 + - - -
125G CYS* 3.6 42.3 - - + +
128G ALA* 3.9 11.9 - - + -
129G VAL* 4.9 0.2 - - + -
177G ALA* 3.9 9.2 - - + +
180G LEU* 3.9 31.2 - - + -
181G THR* 3.7 18.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 86 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ASP* 5.0 1.4 + - - -
93F ARG* 3.4 45.0 - - - +
126F ASP* 3.4 27.4 - - - +
82G GLY 2.7 20.7 + - - +
83G GLU* 2.5 49.5 + - - +
85G VAL* 1.3 71.3 - - - +
87G GLN* 1.3 71.3 + - - +
89G GLY* 3.2 4.5 + - - -
90G ASP* 3.0 47.7 + - - +
93G ARG* 5.8 0.2 + - - -
125G CYS* 5.1 0.9 - - - -
126G ASP* 4.7 12.9 - - - +
129G VAL* 3.7 24.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 87 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G GLU* 2.9 41.5 + - - +
84G ILE* 3.0 10.3 + - - +
86G ARG* 1.3 83.5 - - - +
88G ILE* 1.3 61.0 + - - +
90G ASP* 3.2 8.2 + - + +
91G ALA* 2.8 30.7 + - - +
208G VAL* 3.8 14.2 - - + +
211G GLN* 5.4 1.7 - - - +
212G ASN* 3.0 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 88 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84G ILE* 3.0 23.9 + - + +
85G VAL* 3.4 13.2 - - + +
87G GLN* 1.3 75.7 - - - +
89G GLY* 1.3 61.6 + - - +
91G ALA* 3.3 1.8 + - - +
92G LEU* 2.9 42.0 + - + +
121G TYR* 3.9 20.0 - - + +
125G CYS* 4.2 2.2 - - - -
176G ASN* 3.9 4.9 - - - +
180G LEU* 3.8 29.2 - - + -
204G ILE* 5.7 1.1 - - + -
205G VAL* 3.9 30.1 - - + -
208G VAL* 4.0 24.2 - - + +
209G LEU* 5.6 1.6 - - + -
219G CYS* 5.1 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 89 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G VAL 3.0 10.9 + - - -
86G ARG 3.2 5.8 + - - -
88G ILE* 1.3 77.6 - - - +
90G ASP* 1.3 57.0 + - - +
92G LEU* 3.6 7.7 + - - +
93G ARG* 3.1 27.9 + - - +
122G VAL* 3.8 17.4 - - - +
125G CYS* 3.7 24.0 - - - -
126G ASP* 5.4 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 90 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86F ARG* 5.0 0.9 + - - -
90F ASP* 4.8 13.9 - - - +
86G ARG* 3.0 34.9 + - - +
87G GLN* 3.2 10.5 + - + +
89G GLY* 1.3 74.4 - - - +
91G ALA* 1.3 63.5 + - - +
92G LEU 3.2 0.4 - - - -
93G ARG* 3.1 33.0 + - - +
94G LYS* 3.1 38.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 91 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G GLN 2.8 20.8 + - - +
88G ILE 3.7 2.5 - - - +
90G ASP* 1.3 73.1 - - - +
92G LEU* 1.3 61.1 + - - +
94G LYS* 3.5 18.5 + - - +
95G LYS* 3.5 17.7 + - - +
204G ILE* 3.7 17.9 - - + +
208G VAL* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88G ILE* 2.9 34.6 + - + +
89G GLY* 3.6 9.0 - - - +
91G ALA* 1.3 75.6 - - - +
93G ARG* 1.3 65.3 + - - +
95G LYS* 3.0 6.9 + - - +
96G ILE* 3.0 23.4 + - - +
99G LEU* 3.9 26.1 - - + +
118G VAL* 4.3 7.9 - - + +
121G TYR* 3.5 53.6 - - + -
122G VAL* 3.9 13.5 - - + +
169G VAL* 5.2 0.2 - - + -
201G VAL* 5.2 5.6 - - + -
204G ILE* 4.3 18.8 - - + -
205G VAL* 5.9 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83F GLU* 5.1 1.4 + - - -
86F ARG* 3.4 43.2 - - - +
86G ARG 5.8 0.2 + - - -
89G GLY 3.1 14.4 + - - +
90G ASP* 3.1 32.6 + - - +
92G LEU* 1.3 75.5 - - - +
94G LYS* 1.3 62.7 + - + +
96G ILE* 3.3 29.9 - - + +
119G GLN* 4.5 9.3 - - - +
122G VAL* 3.4 34.2 - - + +
123G ASP* 5.3 1.2 + - - -
126G ASP* 3.1 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 94 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G ASP* 3.1 25.6 + - - +
91G ALA* 3.7 13.5 - - - +
92G LEU 3.2 0.2 - - - -
93G ARG* 1.3 77.8 - - + +
95G LYS* 1.3 65.6 + - + +
96G ILE* 3.7 1.6 + - - +
97G LYS 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 95 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G GLU* 3.3 31.3 + - + +
16G LEU* 4.5 5.6 - - + +
91G ALA 3.5 12.5 + - - +
92G LEU 3.0 8.2 + - - +
94G LYS* 1.3 82.8 - - + +
96G ILE* 1.3 65.4 + - - +
97G LYS 3.2 3.0 + - - -
98G VAL* 3.4 20.3 - - + +
99G LEU* 3.0 23.6 + - + +
204G ILE* 4.1 30.3 - - + -
207G GLU* 6.0 1.8 - - - -
----------------------------------------------------------
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