Contacts of the helix formed by residues 95 - 110 (chain F) in PDB entry 3J8B
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 95 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F LEU* 1.3 76.2 - - - +
96F PRO* 1.3 66.7 - - - +
97F VAL* 4.1 8.7 - - + +
98F ILE* 3.0 19.2 + - - +
99F LEU* 3.5 4.3 + - - +
131F VAL 2.9 18.1 + - - +
132F THR* 4.1 21.3 - - - +
240F ALA 3.4 13.0 + - - +
241F TYR* 5.4 3.8 - - + -
245F GLU* 5.9 5.2 - - + -
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Residues in contact with PRO 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU 3.8 2.2 - - - -
95F HIS* 1.3 71.3 - - - +
97F VAL* 1.3 62.9 + - - +
99F LEU* 3.1 11.5 + - + +
100F ALA* 3.1 22.1 + - - +
239F TYR* 5.7 3.9 - - + -
240F ALA 4.3 3.8 - - - -
241F TYR* 5.3 9.4 - - + -
245F GLU* 5.5 6.9 - - + +
249F VAL* 5.2 10.3 - - + -
214H LEU 5.5 3.4 - - - +
215H MET* 5.5 10.3 - - - -
218H LEU* 5.2 15.9 - - + +
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F HIS* 3.1 9.6 - - + +
96F PRO* 1.3 78.6 - - - +
98F ILE* 1.3 52.4 + - - +
100F ALA* 3.6 6.5 - - - +
101F SER* 2.7 37.4 + - - -
132F THR 4.8 7.6 - - - +
133F ASN* 6.1 1.1 - - - -
245F GLU* 5.9 5.8 - - + +
44H LEU* 5.6 2.1 - - - +
47H LEU* 5.1 17.3 - - + -
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Residues in contact with ILE 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU* 5.3 5.4 - - + -
95F HIS* 3.0 19.8 + - + +
97F VAL* 1.3 78.8 - - - +
99F LEU* 1.3 58.0 + - - +
101F SER* 3.3 6.5 + - - -
102F ILE* 2.9 31.0 + - - +
120F LEU* 6.6 0.2 - - + -
131F VAL* 4.8 10.8 - - + +
132F THR 5.2 0.6 + - - -
133F ASN* 4.9 20.2 - - - +
134F CYS* 5.0 9.3 - - + +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94F LEU* 6.2 0.4 - - + +
95F HIS 3.5 4.6 + - - +
96F PRO* 3.1 13.8 + - + +
98F ILE* 1.3 79.5 - - - +
100F ALA* 1.3 56.4 - - - +
102F ILE* 3.4 5.8 + - - +
103F VAL* 3.1 26.9 + - - +
202F VAL* 5.5 6.3 - - - -
212F SER* 5.4 11.0 - - - -
214H LEU* 4.4 23.6 - - + +
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Residues in contact with ALA 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F PRO 3.1 12.5 + - - +
97F VAL* 3.8 6.5 - - - +
99F LEU* 1.3 78.1 - - - +
101F SER* 1.3 59.1 + - - +
103F VAL* 3.4 6.8 + - - +
104F ASP* 2.9 29.9 + - - +
43H GLY* 5.4 3.1 - - - -
44H LEU* 4.9 20.0 - - + +
211H ILE* 5.9 7.9 - - + +
214H LEU* 5.2 6.2 - - + +
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Residues in contact with SER 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F VAL 2.7 22.1 + - - -
98F ILE* 3.7 7.0 - - - -
100F ALA* 1.3 70.5 - - - +
102F ILE* 1.3 66.1 + - - +
104F ASP* 3.3 6.6 + - - +
105F SER* 2.9 24.8 + - - -
134F CYS* 4.8 18.2 - - - -
44H LEU* 5.0 8.2 - - - +
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Residues in contact with ILE 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98F ILE 2.9 17.5 + - - +
99F LEU 3.8 4.0 - - - +
101F SER* 1.3 75.0 - - - +
103F VAL* 1.3 64.0 + - - +
105F SER* 3.4 8.2 + - - -
106F TYR* 3.1 22.5 + - - +
116F VAL* 5.7 0.7 - - - +
134F CYS* 6.0 0.6 - - - +
173F TYR* 5.7 7.4 - - + -
174F ALA 6.4 1.1 - - - -
175F THR* 5.9 4.1 - - - -
202F VAL* 3.9 27.1 - - + -
204F THR* 5.0 4.6 - - - -
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Residues in contact with VAL 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F LEU 3.1 17.4 + - - +
100F ALA* 3.8 7.4 - - - +
101F SER 3.2 0.2 - - - -
102F ILE* 1.3 76.1 - - - +
104F ASP* 1.3 56.0 + - - +
106F TYR* 3.2 3.6 + - - +
107F GLU* 2.8 31.5 + - - +
204F THR* 4.3 23.5 - - - +
210H LEU* 5.6 9.4 - - + -
211H ILE* 5.8 9.2 - - + +
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Residues in contact with ASP 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F ALA 2.9 17.9 + - - +
101F SER* 3.7 7.2 - - - +
103F VAL* 1.3 76.4 - - - +
105F SER* 1.3 63.1 + - - +
107F GLU* 3.8 7.1 - - - +
108F ARG* 3.4 22.2 + - - +
44H LEU* 5.0 10.5 - - + -
79H THR 5.5 6.1 - - - +
112H ILE* 5.7 1.4 - - - +
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Residues in contact with SER 105 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER 2.9 17.9 + - - -
102F ILE* 3.5 9.0 - - - -
104F ASP* 1.3 78.2 - - - +
106F TYR* 1.3 63.1 + - - +
108F ARG* 3.7 0.7 + - - -
109F ARG* 4.9 0.9 - - - +
116F VAL* 4.9 13.4 - - - +
136F SER* 4.4 23.3 - - - -
111H ASN* 3.4 28.3 - - - +
112H ILE 6.2 0.4 - - - +
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Residues in contact with TYR 106 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F ILE 3.1 11.1 + - - +
103F VAL 3.6 7.2 - - - +
105F SER* 1.3 81.4 - - - +
107F GLU* 1.3 63.3 + - - +
108F ARG 3.4 0.3 + - - -
109F ARG* 3.6 12.7 + - - +
110F ASN* 3.7 7.8 + - - -
111F GLU 4.6 5.4 + - - +
116F VAL* 4.5 17.2 - - + +
175F THR* 4.9 8.7 - - - -
204F THR* 4.5 16.6 - - - -
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Residues in contact with GLU 107 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F VAL 2.8 21.5 + - - +
104F ASP* 3.8 9.2 - - - +
105F SER 3.3 0.2 - - - -
106F TYR* 1.3 73.7 - - - +
108F ARG* 1.3 64.8 + - - +
110F ASN* 3.1 17.3 + - - +
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Residues in contact with ARG 108 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104F ASP 3.4 11.2 + - - +
105F SER* 5.4 0.2 - - - -
106F TYR 3.4 1.2 - - - -
107F GLU* 1.3 79.5 - - - +
109F ARG* 1.3 62.5 + - - +
110F ASN* 4.4 2.6 - - - +
111H ASN* 3.3 11.6 - - + +
112H ILE* 3.3 44.6 - - + +
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Residues in contact with ARG 109 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F SER 4.9 1.1 - - - +
106F TYR* 3.6 8.0 + - - +
107F GLU 3.3 0.6 - - - -
108F ARG* 1.3 80.4 - - - +
110F ASN* 1.3 70.2 + - - +
111F GLU* 4.3 13.4 - - + +
114F ALA* 5.8 3.4 - - + -
111H ASN* 3.4 18.4 - - + +
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Residues in contact with ASN 110 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F TYR 3.7 3.7 + - - -
107F GLU* 3.1 16.3 + - - +
108F ARG 4.4 2.7 - - - +
109F ARG* 1.3 82.8 - - - +
111F GLU* 1.3 60.4 + - - +
112F GLY 4.2 1.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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