Contacts of the helix formed by residues 77 - 95 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142F SER 3.5 20.2 - - - +
143F GLU* 3.6 24.0 - - - +
144F ARG 4.0 0.7 - - - +
145F PRO* 3.7 33.9 - - + -
75H ASP 3.4 9.6 - - - +
76H ILE* 1.3 92.7 - - + +
78H ALA* 1.3 66.0 + - - +
79H PRO* 4.1 0.9 - - + -
80H LYS* 3.1 15.5 + - + +
81H ARG* 3.0 18.4 + - - +
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Residues in contact with ALA 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F PRO* 3.9 16.5 - - + +
142F SER 4.4 1.2 + - - -
76H ILE 3.6 0.8 + - - -
77H PRO* 1.3 72.2 - - - +
79H PRO* 1.4 63.1 - - + +
81H ARG* 3.1 34.1 + - - +
82H GLY 2.9 23.9 + - - -
132H SER* 3.2 23.2 - - - +
135H ILE* 4.2 10.1 - - + -
181H THR 4.0 5.7 - - - +
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Residues in contact with PRO 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F PRO 3.7 13.2 - - - +
142F SER 3.5 15.0 - - - +
143F GLU* 3.7 24.7 - - + -
77H PRO 3.5 2.9 - - - -
78H ALA* 1.4 89.8 - - + +
80H LYS* 1.3 55.5 + - - +
82H GLY* 3.2 2.6 + - - -
83H GLU* 3.1 23.7 + - - +
132H SER* 3.5 26.1 + - - +
133H ARG* 3.5 39.8 + - + +
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Residues in contact with LYS 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F GLU* 3.1 35.4 + - + +
144F ARG* 5.3 0.2 - - - +
145F PRO* 5.2 8.5 - - + +
76H ILE* 3.7 15.3 - - + +
77H PRO* 3.1 22.5 + - + +
79H PRO* 1.3 78.6 - - + +
81H ARG* 1.3 64.4 + - - +
83H GLU* 3.4 20.9 - - + +
84H ILE* 3.5 12.6 + - - +
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Residues in contact with ARG 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444G PRO* 6.1 0.4 - - - +
73H TRP* 3.6 38.4 + - + -
74H ALA 4.0 13.1 + - - -
76H ILE* 2.9 28.7 + - + +
77H PRO* 3.0 16.8 + - - +
78H ALA* 3.1 29.4 + - - +
80H LYS* 1.3 74.2 - - - +
82H GLY* 1.3 59.6 + - - +
84H ILE* 3.1 8.6 + - - +
85H VAL* 3.0 28.8 + - - +
135H ILE* 4.7 2.0 - - - +
155H PRO* 4.6 8.5 - - - +
180H LEU 3.2 19.3 - - - +
181H THR* 2.6 34.0 + - - +
182H CYS* 3.5 4.0 - - - +
183H GLY* 3.1 27.0 - - - +
488H MET* 5.6 1.8 - - - +
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Residues in contact with GLY 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78H ALA 2.9 10.1 + - - -
79H PRO 3.2 6.0 + - - -
81H ARG* 1.3 75.3 - - - +
83H GLU* 1.3 53.7 + - - +
85H VAL* 3.1 9.0 + - - -
86H ARG* 2.7 35.2 + - - +
129H VAL* 3.5 17.1 - - - +
132H SER* 3.8 20.8 - - - -
181H THR* 4.8 2.9 + - - -
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Residues in contact with GLU 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ARG* 5.1 1.8 + - - -
123E ASP* 5.7 1.0 - - - +
79H PRO 3.1 11.2 + - - +
80H LYS* 3.4 16.8 - - + +
81H ARG 3.2 0.4 - - - -
82H GLY* 1.3 73.3 - - - +
84H ILE* 1.3 67.4 + - + +
86H ARG* 2.6 43.5 + - - +
87H GLN* 2.9 42.1 + - - +
129H VAL* 6.0 0.7 - - - -
212H ASN* 5.8 0.2 - - - +
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Residues in contact with ILE 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H TRP* 4.0 17.7 - - + -
76H ILE* 6.3 0.7 - - + -
80H LYS 3.5 13.4 + - - +
81H ARG 3.1 8.8 + - - +
83H GLU* 1.3 79.5 - - + +
85H VAL* 1.3 63.1 + - - +
87H GLN* 3.0 18.1 + - - +
88H ILE* 3.0 21.3 + - + +
180H LEU* 5.4 2.9 - - + -
208H VAL* 4.5 10.8 - - + -
209H LEU* 4.1 25.8 - - + -
212H ASN* 3.5 34.8 - - + +
214H LEU* 3.7 20.4 - - + -
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Residues in contact with VAL 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H ARG 3.0 13.2 + - - +
82H GLY* 3.1 9.6 + - - +
84H ILE* 1.3 75.2 - - + +
86H ARG* 1.3 63.2 + - - +
88H ILE* 3.3 10.7 + - + +
89H GLY 3.0 17.2 + - - -
125H CYS* 3.6 41.9 - - - +
128H ALA* 3.9 12.1 - - + -
129H VAL* 4.8 0.4 - - + -
177H ALA* 4.0 8.5 - - + +
180H LEU* 3.9 31.6 - - + -
181H THR* 3.7 17.5 - - - +
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E ASP* 5.1 1.6 + - - -
93E ARG* 3.5 43.4 - - - +
126E ASP* 3.5 26.5 - - - -
82H GLY 2.7 19.8 + - - +
83H GLU* 2.6 49.8 + - - +
85H VAL* 1.3 72.7 - - - +
87H GLN* 1.3 70.1 + - - +
89H GLY* 3.1 4.8 + - - -
90H ASP* 3.0 48.2 + - - +
93H ARG* 5.8 0.3 + - - -
125H CYS* 5.1 0.9 - - - -
126H ASP* 4.7 12.3 - - - +
129H VAL* 3.7 23.3 - - + +
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Residues in contact with GLN 87 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H GLU* 2.9 40.9 + - - +
84H ILE* 3.0 9.8 + - - +
86H ARG* 1.3 83.9 - - - +
88H ILE* 1.3 55.7 + - - +
90H ASP* 3.1 8.5 + - + +
91H ALA* 2.8 35.9 + - - +
208H VAL* 3.8 14.2 - - + +
211H GLN* 5.4 1.7 - - - +
212H ASN* 3.0 37.1 + - - +
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Residues in contact with ILE 88 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H ILE* 3.0 24.3 + - + +
85H VAL* 3.3 13.0 + - + +
87H GLN* 1.3 74.9 - - - +
89H GLY* 1.3 63.8 + - - +
91H ALA* 3.3 1.7 + - - +
92H LEU* 3.0 41.6 + - + +
121H TYR* 3.9 20.6 - - + +
125H CYS* 4.2 2.9 - - - -
176H ASN* 3.9 4.5 - - - +
180H LEU* 3.8 28.7 - - + -
204H ILE* 4.9 1.5 - - + +
205H VAL* 3.9 30.5 - - + -
208H VAL* 4.0 24.4 - - + +
209H LEU* 5.6 2.0 - - + -
219H CYS* 5.1 0.2 - - - -
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Residues in contact with GLY 89 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85H VAL 3.0 10.7 + - - -
86H ARG 3.1 5.8 + - - -
88H ILE* 1.3 77.7 - - - +
90H ASP* 1.3 57.4 + - - +
92H LEU* 3.5 7.6 + - - +
93H ARG* 3.1 28.2 + - - +
122H VAL* 3.8 16.9 - - - +
125H CYS* 3.8 23.5 - - - -
126H ASP* 5.4 1.6 - - - -
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Residues in contact with ASP 90 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E ARG* 5.1 0.7 + - - -
90E ASP* 4.9 13.0 - - - +
86H ARG* 3.0 36.3 + - - +
87H GLN* 3.1 10.5 + - + +
89H GLY* 1.3 75.4 - - - +
91H ALA* 1.3 63.7 + - - +
93H ARG* 3.1 31.8 + - - +
94H LYS* 3.1 39.1 + - - +
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Residues in contact with ALA 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H GLN 2.8 19.5 + - - +
88H ILE 3.8 2.0 - - - +
90H ASP* 1.3 72.7 - - - +
92H LEU* 1.3 62.1 + - - +
94H LYS* 3.4 20.7 + - - +
95H LYS* 3.5 17.8 + - - +
204H ILE* 3.7 18.7 - - + +
208H VAL* 3.6 23.1 - - + -
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Residues in contact with LEU 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H ILE* 3.0 35.0 + - + +
89H GLY* 3.6 9.0 - - - +
91H ALA* 1.3 76.2 - - - +
93H ARG* 1.3 65.0 + - - +
95H LYS* 3.0 7.3 + - - -
96H ILE* 3.0 23.2 + - - +
99H LEU* 3.9 27.0 - - + +
118H VAL* 4.2 8.5 - - + +
121H TYR* 3.5 51.6 - - + -
122H VAL* 3.9 12.8 - - + +
169H VAL* 5.2 0.7 - - + -
201H VAL* 5.2 5.2 - - + -
204H ILE* 4.3 18.8 - - + -
205H VAL* 5.9 0.9 - - + -
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Residues in contact with ARG 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E GLU* 5.2 1.0 + - - -
86E ARG* 3.5 42.0 - - - +
86H ARG 5.8 0.4 + - - -
89H GLY 3.1 13.6 + - - +
90H ASP* 3.2 32.9 + - - +
92H LEU* 1.3 75.5 - - - +
94H LYS* 1.3 61.5 + - + +
96H ILE* 3.2 30.3 - - + +
119H GLN* 4.4 9.5 - - - +
122H VAL* 3.4 35.2 - - + +
123H ASP* 5.3 1.2 + - - -
126H ASP* 3.2 31.1 + - - -
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Residues in contact with LYS 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H ASP* 3.1 25.1 + - - +
91H ALA* 3.6 14.8 - - - +
92H LEU 3.2 0.4 - - - -
93H ARG* 1.3 76.5 - - + +
95H LYS* 1.3 66.9 + - + +
96H ILE* 3.8 1.4 + - - +
97H LYS 5.4 0.2 + - - -
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Residues in contact with LYS 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H GLU* 3.3 30.8 + - + +
16H LEU* 4.4 5.6 - - + +
91H ALA 3.5 13.4 + - - +
92H LEU 3.0 8.2 + - - +
94H LYS* 1.3 82.4 - - + +
96H ILE* 1.3 64.2 + - - +
97H LYS 3.2 3.0 + - - -
98H VAL* 3.4 19.6 - - + +
99H LEU* 3.0 23.9 + - + +
204H ILE* 4.1 30.1 - - + -
207H GLU* 6.0 1.6 - - - -
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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