Contacts of the helix formed by residues 97 - 110 (chain B) in PDB entry 1EQB
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 SER 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96A HIS* 4.0 15.4 + - - -
262A GLY 5.1 0.2 + - - -
263A GLY 5.4 1.1 - - - -
265A LEU* 6.1 1.6 - - - -
95B PRO* 3.2 1.9 - - - +
96B HIS* 1.3 80.7 - - - +
98B GLY* 1.3 61.1 + - - +
99B SER* 3.5 4.0 + - - -
100B GLN* 2.6 33.6 + - - +
101B ALA* 3.0 22.0 + - - +
235B ARG 6.0 0.2 - - - -
236B GLY* 3.7 3.8 - - - -
237B GLY* 3.3 21.9 - - - +
2291B PLP 3.5 18.4 + - - -
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Residues in contact with GLY 98 (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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97B SER* 1.3 72.7 - - - +
99B SER* 1.3 65.3 + - - +
101B ALA* 3.2 6.2 + - - +
102B ASN* 2.9 29.2 + - - +
224B THR* 6.5 0.2 - - - -
225B THR 5.0 2.2 - - - -
226B THR* 3.5 21.0 - - - +
237B GLY* 4.5 1.6 - - - -
2291B PLP 3.3 30.1 + - - -
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Residues in contact with SER 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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260A GLY 4.2 4.7 - - - -
261A GLN* 3.6 13.4 - - - -
262A GLY* 3.2 21.8 + - - -
97B SER* 3.3 3.8 - - - -
98B GLY* 1.3 75.7 - - - +
100B GLN* 1.3 60.7 + - - +
102B ASN* 3.3 4.1 + - - +
103B PHE* 2.8 29.3 + - - +
126B HIS* 4.4 1.0 - - - -
128B THR* 3.9 27.0 - - - +
134B ASN* 5.9 0.2 - - - -
135B PHE* 4.1 5.5 - - - -
2291B PLP 2.9 23.3 + - - -
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Residues in contact with GLN 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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96A HIS* 3.5 14.1 - - - -
100A GLN* 3.5 40.5 - - - +
103A PHE* 6.3 1.4 - - - -
260A GLY 3.2 23.0 + - - -
261A GLN* 4.1 4.0 - - - +
95B PRO* 4.4 2.1 - - - +
96B HIS* 4.0 5.4 - - + +
97B SER* 2.6 35.9 + - - +
98B GLY 3.2 0.4 - - - -
99B SER* 1.3 80.1 - - - +
101B ALA* 1.3 66.1 + - - +
103B PHE* 3.3 13.8 + - + +
104B ALA* 3.0 22.9 + - - +
261B GLN* 3.4 28.9 - - + +
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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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95B PRO* 3.8 23.0 - - + +
97B SER 3.0 17.1 + - - +
98B GLY* 3.2 6.7 + - - +
100B GLN* 1.3 77.5 - - - +
102B ASN* 1.3 63.8 + - - +
104B ALA* 3.2 12.4 + - - +
105B VAL* 3.2 16.3 + - - +
224B THR* 4.0 20.1 - - + +
225B THR 4.9 0.9 - - - +
237B GLY* 4.3 0.4 - - - -
238B LEU 4.0 16.8 - - - +
239B ILE* 4.2 4.1 - - + +
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Residues in contact with ASN 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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98B GLY 2.9 16.6 + - - +
99B SER 3.6 7.0 - - - +
101B ALA* 1.3 73.9 - - - +
103B PHE* 1.3 65.7 + - - +
105B VAL* 3.1 4.5 + - - +
106B TYR* 2.9 38.7 + - + -
128B THR* 2.7 31.9 + - - +
129B HIS* 4.2 4.4 + - - -
135B PHE* 4.8 0.4 - - + -
198B PHE* 3.3 16.8 - - + -
200B ASP* 2.9 21.8 + - - +
224B THR* 2.7 29.1 + - - -
2291B PLP 3.8 5.6 - - - -
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Residues in contact with PHE 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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100A GLN* 6.2 1.3 - - - -
103A PHE* 3.7 38.1 - + - -
135A PHE* 4.5 13.5 - - + -
139A LEU* 5.2 3.4 - - + -
99B SER 2.8 20.5 + - - +
100B GLN* 3.6 17.9 - - + +
102B ASN* 1.3 71.7 - - - +
104B ALA* 1.3 67.3 + - - +
106B TYR* 3.3 2.8 + - - +
107B THR* 3.0 53.2 + - + +
135B PHE* 3.5 43.3 - + + -
139B LEU* 4.6 7.4 - - + -
255B ALA 5.5 0.4 - - - -
259B GLY 5.2 0.7 - - - -
260B GLY* 4.3 26.7 - - - -
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Residues in contact with ALA 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 GLN 3.0 12.5 + - - +
101B ALA* 3.3 10.3 - - - +
103B PHE* 1.3 80.5 - - + +
105B VAL* 1.3 63.9 + - - +
107B THR* 3.2 9.3 + - - -
108B ALA* 2.9 26.6 + - - +
239B ILE* 4.1 6.7 - - + -
252B LEU* 5.1 1.1 - - + -
255B ALA* 3.4 13.9 - - + +
256B VAL* 3.8 31.9 - - + +
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Residues in contact with VAL 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 3.6 4.3 - - - +
102B ASN 3.1 7.9 + - - +
104B ALA* 1.3 77.4 - - - +
106B TYR* 1.3 63.9 + - - +
108B ALA* 4.0 0.2 - - - -
109B LEU* 3.2 32.6 + - + +
169B MET* 3.8 20.8 - - + +
198B PHE* 3.9 25.1 - - + -
222B VAL* 3.8 20.9 - - + -
224B THR* 3.5 31.9 - - + -
239B ILE* 4.6 4.0 - - + -
252B LEU* 4.4 13.2 - - + -
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Residues in contact with TYR 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 ASN* 2.9 41.8 + - + -
103B PHE* 3.6 5.8 - - - +
105B VAL* 1.3 76.6 - - - +
107B THR* 1.3 60.0 + - + +
108B ALA 3.2 0.2 + - - -
110B LEU* 2.8 50.6 + - + +
116B VAL* 4.6 12.7 - - + +
128B THR 2.4 30.9 + - - -
129B HIS* 3.8 2.4 - - - -
130B GLY 4.1 0.2 + - - -
135B PHE* 3.8 17.7 - + + -
136B SER* 3.6 11.6 - - - -
140B TYR* 3.5 42.0 - + + +
142B ILE* 5.3 2.3 - - + +
169B MET* 5.0 5.4 - - - -
171B ILE* 3.1 29.2 - - + +
198B PHE* 4.5 9.6 - + - -
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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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135A PHE* 5.9 2.5 - - + -
138A LYS* 5.7 9.4 - - - +
139A LEU* 5.8 8.1 - - + -
103B PHE* 3.0 50.4 + - + +
104B ALA* 3.2 10.7 + - - -
106B TYR* 1.3 79.4 - - + +
108B ALA* 1.3 59.2 + - - +
109B LEU 3.5 0.2 - - - -
110B LEU 4.0 10.6 - - - +
111B GLU* 5.6 0.5 - - - +
139B LEU* 5.8 1.8 - - + -
140B TYR* 3.9 14.8 - - - +
255B ALA* 4.0 11.2 + - - +
259B GLY* 6.0 0.7 - - - -
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Residues in contact with ALA 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 ALA 2.9 16.7 + - - +
105B VAL 4.0 1.8 - - - +
106B TYR 3.1 0.2 - - - -
107B THR* 1.3 78.9 - - - +
109B LEU* 1.3 67.6 + - + +
110B LEU 5.1 0.2 - - - -
251B LYS* 3.7 37.9 + - + +
252B LEU* 4.0 19.3 - - + -
255B ALA* 3.4 19.1 - - + -
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Residues in contact with LEU 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 VAL* 3.2 25.0 + - + +
108B ALA* 1.3 91.1 - - + +
110B LEU* 1.3 67.3 + - - +
168B LYS* 4.0 11.6 + - - -
169B MET* 3.5 29.2 - - + -
196B TYR* 4.0 44.5 - - + +
198B PHE* 5.7 0.9 - - + -
222B VAL* 4.0 19.7 - - + -
248B LEU* 3.5 29.4 - - + -
251B LYS* 5.4 3.4 - - + -
252B LEU* 5.2 1.8 - - + -
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Residues in contact with LEU 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 TYR* 2.8 32.2 + - + +
107B THR* 4.0 13.0 - - - +
109B LEU* 1.3 87.1 - - + +
111B GLU* 1.3 71.5 + - - +
112B PRO* 4.6 1.6 - - - +
114B ASP* 3.4 7.0 - - + +
116B VAL* 3.4 30.5 - - + -
140B TYR* 4.0 16.9 + - + -
168B LYS* 3.4 42.2 - - + +
169B MET* 4.0 30.7 - - + -
196B TYR* 5.0 0.9 - - + -
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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