Contacts of the helix formed by residues 101 - 118 (chain X) in PDB entry 3G90
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 ASN 101 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98X PRO 3.8 0.5 + - - +
99X PHE 3.9 3.8 - - - +
100X GLN* 1.3 84.4 + - - +
102X GLN* 1.3 59.2 - - - +
103X THR* 3.2 8.8 + - - -
104X HIS* 2.8 57.1 + - - -
105X ALA* 3.0 30.9 + - - +
218X PHE 5.1 3.8 + - - +
219X MET* 4.1 15.5 - - - +
220X MET 5.6 1.6 - - - +
387X ILE* 5.2 4.0 - - - -
390X TRP* 5.3 1.3 - - - -
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Residues in contact with GLN 102 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X ASN* 1.3 76.3 - - - +
103X THR* 1.3 59.4 + - - +
105X ALA* 4.3 0.2 - - - -
106X LYS* 2.9 45.2 + - + +
383X ARG 4.3 2.4 - - - +
384X GLU* 3.8 19.9 + - - +
385X HIS 3.1 34.7 + - - +
386X THR* 5.3 1.5 - - - +
387X ILE* 6.6 0.2 - - + -
390X TRP* 3.4 22.9 + - + +
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Residues in contact with THR 103 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101X ASN* 3.2 8.3 + - - +
102X GLN* 1.3 76.3 - - - +
104X HIS* 1.3 66.0 + - + +
106X LYS* 4.1 5.5 - - - +
107X ARG* 3.2 27.7 + - + +
217X SER* 3.6 35.3 + - - +
218X PHE 4.2 2.1 + - - -
219X MET* 3.8 33.7 - - + -
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Residues in contact with HIS 104 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98X PRO* 3.2 20.6 - - + +
100X GLN* 3.9 21.8 - - + +
101X ASN* 2.8 33.4 + - - +
103X THR* 1.3 78.1 - - + +
105X ALA* 1.3 57.1 + - - +
107X ARG* 4.1 8.6 - - - +
108X ALA* 3.1 29.8 + - - +
219X MET* 3.5 30.1 - - + +
221X THR* 4.9 5.4 + - - +
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Residues in contact with ALA 105 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98X PRO 3.1 12.7 + - - +
99X PHE* 3.9 5.2 - - - -
101X ASN 3.0 19.4 + - - +
102X GLN 4.0 0.7 - - - +
103X THR 3.2 0.2 - - - -
104X HIS* 1.3 75.6 - - - +
106X LYS* 1.3 65.1 + - - +
109X TYR* 3.0 27.2 + - - +
390X TRP* 3.4 43.1 - - + -
394X ILE* 3.9 8.2 - - + +
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Residues in contact with LYS 106 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X GLN* 2.9 33.6 + - + +
103X THR* 4.1 5.4 - - - +
105X ALA* 1.3 76.5 - - - +
107X ARG* 1.3 56.9 + - - +
109X TYR* 3.8 2.0 - - - +
110X ARG* 2.9 34.2 + - - +
211X ALA* 4.7 25.4 - - + +
381X ASP 4.7 3.8 + - - -
382X GLU* 3.8 7.8 - - - +
383X ARG* 2.6 43.4 + - - +
384X GLU* 5.0 1.6 - - - +
390X TRP* 3.6 21.5 - - + -
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Residues in contact with ARG 107 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLN* 5.2 8.9 - - - +
93X LYS* 5.3 7.8 - - - +
103X THR* 3.2 19.3 + - + +
104X HIS* 4.2 8.7 - - - +
106X LYS* 1.3 78.3 - - - +
108X ALA* 1.3 58.2 + - - +
110X ARG* 3.3 5.9 + - - +
111X GLU* 2.8 41.8 + - + +
189X ASP* 5.3 5.7 + - - -
194X ASN* 4.9 4.0 + - - +
207X ASP* 2.9 38.4 + - - +
209X GLY 3.5 22.4 + - - +
210X LEU* 5.4 5.1 - - - +
211X ALA* 5.8 2.7 - - - +
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Residues in contact with ALA 108 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X LEU* 4.3 18.0 - - + +
98X PRO* 3.7 24.0 - - + -
104X HIS 3.1 21.0 + - - +
105X ALA 4.0 2.0 - - - +
107X ARG* 1.3 77.2 - - - +
109X TYR* 1.3 57.3 + - - +
111X GLU* 3.4 12.7 + - - +
112X LEU* 3.0 34.3 + - + +
394X ILE* 4.3 7.4 - - + -
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Residues in contact with TYR 109 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105X ALA 3.0 18.4 + - - +
106X LYS 3.9 2.7 - - - +
108X ALA* 1.3 74.8 - - - +
110X ARG* 1.3 63.2 + - - +
112X LEU* 3.4 4.6 + - - +
113X VAL* 3.1 55.3 + - + +
381X ASP* 4.6 10.8 - - - -
383X ARG* 4.0 35.7 + - - -
390X TRP* 4.0 20.4 - + + -
393X LEU* 3.9 44.8 - - + +
394X ILE* 4.3 13.6 - - + +
397X GLU* 4.4 16.3 + - + -
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Residues in contact with ARG 110 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X LYS* 2.9 17.7 + - - +
107X ARG* 3.8 5.5 - - - +
109X TYR* 1.3 78.2 - - + +
111X GLU* 1.3 65.2 + - - +
113X VAL* 4.8 2.9 - - - -
114X LEU* 3.1 47.8 + - + +
185X ILE* 3.8 19.8 - - - +
186X ILE 4.8 4.0 + - - -
208X PHE* 3.0 38.1 + - - +
209X GLY 3.6 14.6 + - - -
210X LEU 3.5 19.5 + - - -
211X ALA* 4.4 18.4 - - - +
381X ASP* 4.4 28.3 + - - +
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Residues in contact with GLU 111 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X GLN* 4.3 4.2 - - - +
93X LYS* 2.8 32.6 + - - +
95X LEU* 4.2 9.4 - - - +
107X ARG* 2.8 25.3 + - + +
108X ALA* 3.6 12.7 + - - +
110X ARG* 1.3 77.8 - - - +
112X LEU* 1.3 56.9 - - - +
115X MET* 3.1 52.7 + - + +
144X LEU* 3.4 23.8 - - + +
146X MET* 5.3 2.9 - - - +
206X LEU 4.9 7.6 - - - +
207X ASP* 5.6 6.3 - - + +
208X PHE* 4.3 14.5 - - + -
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Residues in contact with LEU 112 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X LEU* 5.7 2.2 - - + -
108X ALA 3.0 20.3 + - - +
109X TYR* 3.6 6.7 - - - +
111X GLU* 1.3 76.2 - - - +
113X VAL* 1.3 62.6 + - - +
115X MET* 5.1 2.7 - - - -
116X LYS* 3.4 37.7 + - - +
126X LEU* 4.4 3.1 - - + +
129X VAL* 3.7 38.6 - - + -
142X VAL* 4.8 4.5 - - + -
144X LEU* 4.0 14.6 - - + +
394X ILE* 4.2 18.4 - - + -
397X GLU* 4.0 25.6 - - + -
398X VAL* 3.8 22.9 - - + -
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Residues in contact with VAL 113 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109X TYR* 3.1 53.0 + - + +
110X ARG* 4.2 3.8 - - - +
112X LEU* 1.3 73.9 - - - +
114X LEU* 1.3 72.5 + - + +
116X LYS* 3.4 6.5 + - - +
117X CYS* 3.3 27.0 + - - +
375X ILE* 5.3 9.2 - - + +
379X GLN* 6.1 4.3 - - + -
381X ASP* 5.3 8.3 - - - +
397X GLU* 4.0 20.6 - - + +
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Residues in contact with LEU 114 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X ARG* 3.1 46.7 + - + +
113X VAL* 1.3 79.0 - - + +
115X MET* 1.3 65.6 + - - +
116X LYS 3.0 1.8 - - - -
117X CYS* 4.5 2.7 - - - -
118X VAL* 3.1 32.4 + - + +
185X ILE* 3.9 20.0 - - + -
208X PHE* 3.8 43.1 - - + -
375X ILE* 3.8 38.4 - - + -
381X ASP* 5.2 6.5 - - - +
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Residues in contact with MET 115 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111X GLU* 3.1 46.9 + - + +
114X LEU* 1.3 78.3 - - - +
116X LYS* 1.3 59.9 + - - +
118X VAL* 3.8 11.8 - - - +
124X ILE* 3.5 43.9 - - + +
125X SER* 5.3 0.7 - - - -
126X LEU* 3.9 40.8 + - + +
144X LEU* 3.8 18.2 - - + -
146X MET* 3.9 19.3 - - - +
206X LEU 5.0 2.7 - - - +
208X PHE* 3.6 18.4 - - + -
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Residues in contact with LYS 116 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112X LEU* 3.4 25.4 + - - +
113X VAL 3.4 9.3 + - - +
114X LEU 3.0 0.6 - - - -
115X MET* 1.3 81.1 - - - +
117X CYS* 1.3 60.6 + - + +
118X VAL 3.6 2.6 + - - +
126X LEU* 3.8 17.5 - - + -
129X VAL* 4.9 7.4 - - - -
397X GLU* 2.8 54.9 + - - +
398X VAL 5.3 0.4 + - - -
400X ASN* 4.2 15.8 + - - +
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Residues in contact with CYS 117 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113X VAL* 3.3 18.0 + - - +
114X LEU* 4.4 5.2 - - - -
116X LYS* 1.3 77.6 - - + +
118X VAL* 1.3 59.0 + - - +
119X ASN* 4.1 2.5 + - - +
373X PRO* 3.6 16.9 - - + +
374X GLN* 4.9 1.8 + - + +
375X ILE* 3.4 49.6 - - - +
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Residues in contact with VAL 118 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X LEU* 3.1 26.4 + - + +
115X MET* 3.8 12.2 - - - +
116X LYS 4.5 2.4 - - - +
117X CYS* 1.3 79.8 - - - +
119X ASN* 1.3 65.5 - - - +
120X HIS 4.1 5.5 + - - +
123X ILE* 4.0 35.8 - - + +
124X ILE 5.5 2.6 - - - +
125X SER* 5.3 4.3 + - - -
179X HIS* 4.2 12.1 - - + -
180X LEU* 4.7 4.3 - - + -
185X ILE* 4.7 7.2 - - + -
208X PHE* 4.3 13.0 - - + -
373X PRO* 3.9 21.8 - - + -
375X ILE* 4.7 7.0 - - + -
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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