Contacts of the helix formed by residues 95 - 108 (chain B) in PDB entry 4DQ6
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 GLY 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93B SER* 2.7 26.1 + - - -
94B PRO* 1.3 82.4 - - - +
96B VAL* 1.3 67.1 + - - +
98B PRO* 3.3 17.4 - - - +
99B ALA* 3.4 1.6 + - - +
245B SER* 3.1 13.8 + - - -
401B PLP 3.5 13.7 - - - -
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Residues in contact with VAL 96 (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 GLY* 1.3 70.4 - - - -
97B ILE* 1.3 69.0 + - + +
99B ALA* 3.2 7.4 + - - +
100B ILE* 3.0 34.6 + - + +
200B ASP* 3.6 30.5 - - - +
202B ILE* 3.8 33.4 - - + -
230B CYS* 3.8 22.9 - - + -
231B MET 4.5 4.5 - - - +
245B SER* 4.3 15.0 - - - -
401B PLP 3.0 18.0 + - + +
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Residues in contact with ILE 97 (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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263A THR 5.8 0.4 - - - +
264A ARG 5.2 0.7 - - - +
266A ASP* 3.6 26.9 - - + +
96B VAL* 1.3 78.0 - - + +
98B PRO* 1.3 63.1 - - + +
100B ILE* 4.4 21.1 - - + +
101B SER* 2.7 30.4 + - - -
121B TYR* 4.1 20.2 - - + +
123B PRO* 3.8 37.9 - - + +
124B PHE* 4.6 6.3 - - + -
127B VAL* 3.8 26.0 - - + -
200B ASP* 5.0 0.2 - - - +
401B PLP 2.9 15.7 + - + +
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Residues in contact with PRO 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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265A ILE* 3.2 30.1 - - + +
266A ASP* 3.6 15.9 - - - +
267A ILE* 4.1 14.8 - - + -
93B SER* 3.9 6.7 - - - +
94B PRO* 4.6 7.9 - - + -
95B GLY* 3.3 26.0 - - - +
97B ILE* 1.3 92.7 - - + +
99B ALA* 1.3 61.5 + - - +
101B SER* 3.3 2.6 + - - -
102B LEU* 3.1 28.4 + - + +
262B PHE* 4.9 4.9 - - + -
401B PLP 3.6 7.4 - - - +
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Residues in contact with ALA 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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93B SER* 3.6 16.5 + - - +
95B GLY 3.4 3.9 + - - +
96B VAL* 3.2 10.2 + - - +
98B PRO* 1.3 78.4 - - - +
100B ILE* 1.3 62.7 + - - +
102B LEU* 3.3 4.1 + - - +
103B LEU* 2.9 28.6 + - - +
230B CYS* 4.4 7.0 - - - -
245B SER* 5.4 0.2 - - - +
247B VAL* 3.5 33.2 - - + -
258B LEU* 4.1 2.3 - - + +
262B PHE* 4.2 11.7 - - + -
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Residues in contact with ILE 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 VAL* 3.0 37.8 + - + +
97B ILE* 3.9 15.9 - - + +
99B ALA* 1.3 74.4 - - - +
101B SER* 1.3 63.6 + - - +
103B LEU* 3.2 8.9 + - - +
104B ILE* 3.0 42.9 + - + +
124B PHE* 4.8 1.8 - - + -
127B VAL* 4.1 13.5 - - + -
166B ILE* 4.1 25.4 - - + -
198B ILE* 3.9 24.5 - - + -
200B ASP* 4.4 11.2 - - + +
230B CYS* 3.9 15.9 - - - -
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Residues in contact with SER 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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264A ARG* 2.7 33.2 + - - +
265A ILE* 3.8 14.1 - - - +
97B ILE 2.7 17.8 + - - -
98B PRO 3.5 4.9 - - - -
100B ILE* 1.3 78.6 - - - +
102B LEU* 1.3 61.6 + - - +
104B ILE* 3.3 4.4 + - - +
105B ASN* 3.1 18.4 + - - +
127B VAL* 3.6 14.6 - - - +
131B ASN* 3.0 22.7 + - - +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ARG* 5.5 2.5 - - - +
265A ILE* 4.3 21.5 - - + -
98B PRO* 3.1 15.8 + - + +
99B ALA 3.3 2.2 + - - +
101B SER* 1.3 75.2 - - - +
103B LEU* 1.3 61.1 + - - +
105B ASN* 3.2 6.6 + - + +
106B GLU* 3.0 26.7 + - - +
258B LEU* 3.7 15.3 - - + -
261B ALA* 3.9 15.7 - - + -
262B PHE* 3.5 48.0 - - + +
264B ARG* 3.8 27.4 - - - +
265B ILE* 3.9 17.9 - - + -
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Residues in contact with LEU 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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99B ALA 2.9 27.2 + - - +
100B ILE* 3.6 7.2 - - - +
102B LEU* 1.3 72.2 - - - +
104B ILE* 1.3 61.9 + - - +
106B GLU* 4.5 2.7 - - + +
107B LEU* 2.8 45.8 + - + +
164B LEU* 4.9 0.4 - - - -
198B ILE* 3.8 28.0 - - + -
228B ILE* 3.8 41.7 - - + -
230B CYS* 4.9 2.9 - - - -
247B VAL* 4.5 9.0 - - + -
249B LEU* 4.1 16.4 - - + -
254B ASP 5.0 2.5 - - - +
257B LEU* 6.4 0.9 - - + -
258B LEU* 4.1 20.0 - - + +
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Residues in contact with ILE 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 ILE* 3.0 38.5 + - + +
101B SER 3.6 4.7 - - - +
102B LEU 3.2 0.2 - - - -
103B LEU* 1.3 74.7 - - - +
105B ASN* 1.3 66.1 + - - +
108B THR* 2.6 30.1 + - - +
114B ILE* 3.7 33.2 - - + -
127B VAL* 3.9 27.6 - - + +
128B VAL* 4.1 9.4 - - + -
131B ASN* 3.8 14.4 - - + +
133B ARG* 3.6 21.8 + - + +
164B LEU* 4.1 15.5 - - + -
166B ILE* 4.3 4.9 - - + -
198B ILE* 5.0 1.3 - - + -
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Residues in contact with ASN 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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264A ARG* 5.6 6.9 + - - +
101B SER 3.1 10.5 + - - +
102B LEU* 3.6 11.2 - - + +
103B LEU 3.2 0.2 - - - -
104B ILE* 1.3 82.7 - - - +
106B GLU* 1.3 80.0 + - - +
108B THR 3.2 15.9 - - - +
131B ASN* 4.2 11.6 - - - +
133B ARG* 3.3 21.4 + - - +
264B ARG* 3.7 13.7 - - - +
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Residues in contact with GLU 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 LEU 3.0 15.8 + - - +
103B LEU* 4.2 4.3 - - + +
105B ASN* 1.3 91.7 + - - +
107B LEU* 1.3 63.2 + - + +
108B THR 3.4 1.4 + - - +
257B LEU* 3.8 58.4 - - + +
258B LEU* 5.1 1.3 - - - +
260B ASP* 6.1 0.3 - - - +
261B ALA* 3.9 13.7 - - + -
264B ARG* 3.0 30.7 + - - -
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Residues in contact with LEU 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 LEU* 2.8 35.1 + - + +
106B GLU* 1.3 78.4 - - + +
108B THR* 1.3 63.4 + - + +
163B LYS* 5.2 2.8 - - - +
164B LEU* 4.1 27.4 - - + +
196B LYS* 4.7 5.8 - - + -
198B ILE* 4.9 1.1 - - + -
228B ILE* 3.8 27.6 - - + -
254B ASP* 3.4 25.4 - - + +
257B LEU* 3.8 22.7 - - + -
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Residues in contact with THR 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 ILE* 2.6 20.4 + - - +
105B ASN 3.2 9.2 - - - +
106B GLU 4.3 1.4 - - - +
107B LEU* 1.3 84.0 - - - +
109B LYS* 1.3 60.3 + - - +
112B ASP* 3.5 18.2 - - + -
114B ILE* 4.6 5.8 - - + -
133B ARG* 2.8 33.5 + - - +
163B LYS* 3.9 17.0 - - + -
164B LEU* 3.7 33.7 - - + -
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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