Contacts of the helix formed by residues 98 - 112 (chain B) in PDB entry 3RIE
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 ASP 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B TYR* 4.7 1.3 - - - -
94B LEU* 5.3 0.2 - - - -
95B THR* 2.8 28.0 + - - +
97B LYS* 1.3 77.7 - - + +
99B GLU* 1.3 70.2 + - - +
100B PHE* 3.0 6.8 + - - -
101B ALA* 3.0 21.1 + - - +
261B ILE* 3.3 14.0 - - + +
262B PRO* 3.2 20.3 - - + +
263B THR* 2.6 43.3 + - - -
234C TRP* 3.5 25.6 - - + -
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Residues in contact with GLU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.2 11.9 - - + +
95B THR 3.1 20.4 + - - +
96B GLU* 3.8 13.1 - - - +
98B ASP* 1.3 83.3 + - - +
100B PHE* 1.3 75.5 + - + +
101B ALA 3.3 0.3 + - - -
102B TYR* 3.4 4.7 + - - +
103B HIS* 2.8 55.8 + - + +
132B ARG* 2.9 36.5 + - - -
162B ASN* 5.9 0.7 - - - +
163B ILE* 3.9 21.2 - - + +
261B ILE* 4.7 5.6 - - - -
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Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU 4.9 3.6 - - - -
97B LYS 3.1 27.6 - - - -
98B ASP* 3.0 3.3 + - - -
99B GLU* 1.3 95.8 + - + +
101B ALA* 1.4 70.6 + - - +
103B HIS 4.6 0.4 - - - +
104B GLU* 2.8 48.9 + - + +
132B ARG* 4.4 8.5 - - - +
297B LYS* 3.5 61.7 - - + -
298B TYR* 3.7 15.5 - - + -
602B GOL 3.8 17.7 - - - -
234C TRP* 3.7 26.2 - + - -
313C PHE* 3.8 8.1 - + - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B ASP 3.0 14.5 + - - +
100B PHE* 1.4 80.2 - - - +
102B TYR* 1.3 62.3 + - - +
105B MET* 3.2 30.7 + - - +
259B ILE* 3.6 4.4 - - + +
260B SER 3.5 20.2 - - - +
261B ILE* 4.3 3.6 - - + -
298B TYR* 3.4 35.3 - - + -
234C TRP* 3.9 9.2 - - + -
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Residues in contact with TYR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.4 5.1 + - - +
100B PHE 3.3 0.2 - - - -
101B ALA* 1.3 77.4 - - - +
103B HIS* 1.3 83.4 + + - +
105B MET 3.4 0.2 + - - -
106B MET* 2.9 63.2 + - + +
130B ILE* 4.7 0.9 - - + -
196B ASP* 2.5 36.5 + - - -
229B GLN* 3.3 32.6 - - + +
259B ILE* 4.2 11.0 - - + -
261B ILE* 3.7 21.5 - - + -
264B TYR* 3.6 26.9 - + - +
269B ILE* 3.8 18.6 - - + -
270B GLY 5.7 0.2 - - - -
501B JFQ 3.4 19.2 + - - -
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Residues in contact with HIS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LEU* 4.2 9.9 - - + -
99B GLU* 2.8 46.3 + - + +
100B PHE 4.5 0.2 - - - +
102B TYR* 1.3 94.9 - + - +
104B GLU* 1.3 62.1 + - - +
107B THR* 2.7 32.1 + - - -
127B ASP* 3.4 14.0 + - - -
129B GLY* 3.8 22.4 - - - +
130B ILE* 3.7 27.0 - - + +
132B ARG* 4.1 7.2 - - - +
133B GLU* 3.7 7.5 - - + +
163B ILE* 4.7 1.3 - - + -
264B TYR* 5.7 0.2 - - - -
501B JFQ 2.9 33.2 + - - -
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PHE* 2.8 36.2 + - + +
101B ALA 4.3 1.1 - - - +
103B HIS* 1.3 77.2 - - - +
105B MET* 1.3 58.3 + - - +
108B HIS* 2.8 46.3 + - + +
133B GLU* 3.6 26.1 - - - +
136B LYS* 5.2 0.5 + - - -
295B ASP 4.7 0.2 - - - +
296B LEU* 3.5 21.1 - - + +
297B LYS* 2.7 28.2 + - - +
298B TYR* 2.8 24.3 + - + -
299B TYR* 3.0 17.3 + - + +
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ALA 3.2 20.4 + - - +
104B GLU* 1.3 73.6 - - - +
106B MET* 1.4 63.0 + - - +
109B VAL* 3.2 49.2 + - + +
258B ASN 5.3 0.2 - - - +
259B ILE* 3.7 26.2 - - + -
271B ILE* 4.0 6.0 - - + +
298B TYR* 3.4 35.7 - - + -
299B TYR* 3.8 22.4 - - - -
303B ASN* 3.8 14.4 - - - +
304B HIS* 4.2 5.8 - - - -
307B ALA* 3.7 30.1 - - + -
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Residues in contact with MET 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B TYR* 2.9 61.4 + - + +
105B MET* 1.4 76.7 - - - +
107B THR* 1.3 58.7 + - - +
110B PRO* 3.1 19.8 - - - +
130B ILE* 3.6 13.7 - - + -
194B ILE* 3.9 21.2 - - + +
195B VAL 3.4 26.5 - - - +
196B ASP* 4.4 2.2 - - + -
227B VAL* 3.3 17.9 - - + +
228B ALA 4.3 1.3 - - - -
229B GLN* 3.7 16.4 - - - +
259B ILE* 4.3 3.6 - - + -
270B GLY 5.1 0.4 - - - +
271B ILE* 4.2 30.1 - - - -
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Residues in contact with THR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B HIS 2.7 21.9 + - - -
104B GLU 4.0 0.7 - - - -
106B MET* 1.3 75.2 - - - +
108B HIS* 1.3 66.8 + - + +
109B VAL 3.3 2.0 - - - -
110B PRO* 3.2 4.3 - - - +
111B MET* 3.0 35.4 + - + +
130B ILE* 3.4 19.4 - - - +
133B GLU* 3.5 30.2 - - + +
134B LEU* 3.5 36.8 - - + +
137B TYR* 4.4 0.2 - - + -
194B ILE* 4.1 5.4 - - + -
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Residues in contact with HIS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B GLU* 2.8 38.6 + - + +
107B THR* 1.3 71.9 - - + +
109B VAL* 1.3 61.9 + - - +
112B THR* 2.8 30.3 + - - +
133B GLU* 2.8 42.9 + - + +
136B LYS* 4.7 0.2 - - + -
137B TYR* 2.6 44.8 + + - +
288B LEU* 3.7 9.6 - - + +
293B PHE* 3.7 12.8 - + - -
296B LEU* 3.6 21.9 - - + +
299B TYR* 3.6 22.8 + - + -
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Residues in contact with VAL 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B MET* 3.2 47.2 + - + +
108B HIS* 1.3 80.2 - - - +
110B PRO* 1.4 67.3 - - + +
112B THR* 3.5 1.0 + - - -
113B VAL* 3.4 12.5 - - - +
227B VAL* 4.9 1.1 - - + -
271B ILE* 4.5 9.6 - - + -
273B CYS* 4.6 8.7 - - - -
281B LEU* 3.8 27.4 - - + +
299B TYR* 4.3 8.3 - - + -
304B HIS* 3.3 30.6 - - + +
307B ALA* 5.8 0.4 - - + -
308B PHE* 4.0 18.4 - - + -
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Residues in contact with PRO 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B MET 3.1 25.6 - - - +
107B THR 3.2 13.7 - - - +
109B VAL* 1.4 92.2 - - + +
111B MET* 1.4 55.7 + - - +
113B VAL* 3.1 2.3 + - - +
114B SER* 2.9 34.3 + - - -
192B VAL* 4.0 29.4 - - + -
194B ILE* 4.4 2.5 - - + -
225B TYR* 4.6 6.5 - - + -
227B VAL* 3.8 26.7 - - + -
281B LEU* 3.7 15.7 - - + +
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Residues in contact with MET 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 3.0 25.2 + - + +
110B PRO* 1.4 79.0 - - + +
112B THR* 1.3 60.2 + - - +
113B VAL 3.3 0.2 - - - -
114B SER* 3.9 5.8 - - - +
117B PRO* 3.5 33.0 - - + +
120B VAL* 3.9 11.9 - - + -
134B LEU* 3.7 29.4 - - + -
137B TYR* 3.3 48.5 - - + +
140B VAL* 3.6 21.8 - - + -
192B VAL* 4.0 15.3 - - + -
194B ILE* 5.1 0.2 - - + -
286B LYS* 3.0 23.0 + - - -
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Residues in contact with THR 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B HIS 2.8 23.1 + - - +
111B MET* 1.3 76.7 - - - +
113B VAL* 1.3 58.4 + - - +
137B TYR* 3.7 2.7 - - - +
284B PRO* 3.4 2.3 - - - +
285B ASN* 2.8 30.0 + - - +
286B LYS* 3.4 27.0 + - + +
288B LEU* 3.6 41.1 - - + -
299B TYR* 3.0 22.7 + - - +
304B HIS* 3.1 15.4 + - - -
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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