Contacts of the helix formed by residues 95 - 109 (chain B) in PDB entry 4IVR
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 GLU 95 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88B TRP 4.0 2.2 - - - -
89B ARG* 2.7 75.3 + - - +
90B VAL* 6.0 0.5 - - - +
94B SER* 1.3 85.0 - - - +
96B THR* 1.3 64.0 + - - +
97B ILE* 3.3 3.5 - - - +
98B ALA* 3.4 17.9 + - + +
99B ASN* 3.1 19.1 + - - +
223B PRO* 4.3 10.4 - - - +
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Residues in contact with THR 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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88B TRP 2.5 28.6 + - - -
93B ALA* 4.1 10.1 - - + +
94B SER 4.4 1.3 - - - -
95B GLU* 1.3 70.2 - - - +
97B ILE* 1.3 66.5 + - - +
99B ASN* 3.2 8.6 + - - +
100B ILE* 2.9 22.6 + - + +
124B ALA* 3.5 31.2 - - + +
127B THR* 3.6 21.8 - - - +
128B MET* 3.5 28.5 - - + -
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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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85B MET* 4.7 15.3 - - + -
88B TRP* 4.3 17.3 - - + -
89B ARG* 5.7 2.9 - - + -
95B GLU* 3.3 1.1 - - - +
96B THR* 1.3 77.9 - - - +
98B ALA* 1.3 61.0 + - - +
100B ILE* 3.1 16.3 + - - +
101B TYR* 3.1 41.8 + - + -
128B MET* 3.5 25.6 - - + -
222B ARG* 4.8 5.6 - - + -
223B PRO 3.3 22.4 - - - +
225B GLU* 3.8 11.7 - - + +
401B N50 3.3 32.1 - - - +
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Residues in contact with ALA 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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95B GLU* 3.4 25.2 + - + +
97B ILE* 1.3 79.3 - - - +
99B ASN* 1.3 57.2 + - - +
101B TYR* 4.1 0.2 - - - -
102B THR* 2.9 38.3 + - - +
223B PRO 4.0 1.5 + - - +
224B GLY* 3.5 29.7 - - - +
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Residues in contact with ASN 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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119A VAL* 6.1 2.6 - - - +
94B SER 5.1 2.9 - - - +
95B GLU 3.1 14.3 + - - +
96B THR* 3.4 10.8 - - - +
97B ILE 3.2 0.2 - - - -
98B ALA* 1.3 73.9 - - - +
100B ILE* 1.3 64.4 + - - +
102B THR* 4.1 4.1 - - - -
103B THR* 2.9 39.8 + - - -
120B VAL* 3.7 15.3 - - - +
124B ALA* 3.8 24.5 - - - +
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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 THR 2.9 18.8 + - - +
97B ILE* 3.4 8.1 - - - +
99B ASN* 1.3 77.9 - - - +
101B TYR* 1.3 60.5 + - + +
103B THR* 3.4 0.8 + - - -
104B GLN 3.1 12.1 + - - -
120B VAL* 5.8 0.9 - - - -
121B MET* 3.1 38.5 - - + +
124B ALA* 3.8 16.8 - - + -
125B GLN* 4.3 14.4 - - + +
128B MET* 3.9 27.4 - - + -
176B ARG* 3.6 33.2 - - + +
401B N50 3.5 27.6 - - - +
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Residues in contact with TYR 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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58B HIS* 3.6 18.7 + - - -
97B ILE* 3.1 29.5 + - + +
100B ILE* 1.3 77.9 - - + +
102B THR* 1.3 65.1 + - - +
103B THR 3.2 1.3 - - - -
104B GLN* 3.9 5.9 - - + +
105B HIS* 3.0 25.1 + - - +
176B ARG* 3.6 23.0 + - - -
224B GLY 3.7 14.1 - - - +
225B GLU* 3.2 39.9 + - + -
226B ARG* 3.5 44.3 - - + +
228B ASP* 4.9 8.5 - - + -
231B MET* 4.8 10.7 - - + +
401B N50 3.7 25.8 + - - -
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Residues in contact with THR 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 ALA* 2.9 25.1 + - - +
99B ASN* 4.1 4.5 - - - -
101B TYR* 1.3 76.4 - - - +
103B THR* 1.3 53.6 + - - +
105B HIS* 3.2 3.5 + - - +
106B ARG* 2.8 75.2 + - + +
224B GLY 5.4 0.3 + - - -
226B ARG* 3.4 30.2 + - - +
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Residues in contact with THR 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 ASN* 2.9 23.3 + - - -
100B ILE 3.5 4.0 - - - -
101B TYR 3.2 0.2 - - - -
102B THR* 1.3 78.7 - - - +
104B GLN* 1.3 66.1 + - - +
106B ARG* 3.5 9.3 + - - +
107B LEU* 3.0 22.2 + - - +
112B ILE* 3.9 10.5 - - + +
117B ALA* 4.0 29.4 - - + +
120B VAL* 3.4 31.0 - - + +
121B MET* 4.3 10.3 - - + -
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Residues in contact with GLN 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 3.1 8.3 + - - +
101B TYR* 3.9 8.7 - - + +
102B THR 3.4 0.2 - - - -
103B THR* 1.3 76.1 - - - +
105B HIS* 1.3 59.1 + - - +
107B LEU* 3.1 14.4 + - - +
108B ASP* 2.8 63.6 + - - +
121B MET* 3.9 5.8 - - + +
176B ARG* 3.1 29.4 + - - +
179B MET* 3.1 46.0 + - + +
181B SER* 2.9 26.2 + - - -
228B ASP* 4.2 6.5 - - - +
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Residues in contact with HIS 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 TYR 3.0 19.5 + - - +
102B THR* 3.3 5.4 + - - +
104B GLN* 1.3 77.7 - - - +
106B ARG* 1.3 63.1 + - - +
108B ASP* 3.1 11.1 + - + +
109B GLN* 2.8 69.6 + - + +
111B GLU* 4.7 7.6 - - - -
226B ARG* 3.1 36.2 + - - +
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Residues in contact with ARG 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 THR* 2.8 47.3 + - + +
103B THR* 4.0 9.4 + - - +
105B HIS* 1.3 77.9 - - - +
107B LEU* 1.3 62.5 + - - +
109B GLN 3.3 1.1 + - - +
110B GLY 3.1 3.6 + - - -
111B GLU* 2.8 60.3 + - + +
112B ILE* 3.6 23.5 + - + -
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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 THR 3.0 14.4 + - - +
104B GLN* 3.1 18.4 + - - +
106B ARG* 1.3 75.4 - - - +
108B ASP* 1.3 65.4 + - - +
110B GLY* 3.2 11.1 + - - -
112B ILE* 3.4 25.6 - - + +
113B SER* 3.7 2.7 - - - +
114B ALA* 3.6 25.6 - - + +
117B ALA* 4.0 18.6 - - + -
179B MET 4.4 1.3 - - - +
180B GLY* 3.6 31.0 - - - +
181B SER* 4.2 6.7 - - - -
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Residues in contact with ASP 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 GLN* 2.8 49.0 + - - +
105B HIS* 3.1 11.8 + - + +
107B LEU* 1.3 80.3 - - - +
109B GLN* 1.3 68.1 + - - +
110B GLY* 3.0 4.9 + - - -
179B MET* 5.0 2.2 - - - +
228B ASP* 4.2 9.2 - - - +
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Residues in contact with GLN 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 HIS* 2.8 61.2 + - + +
108B ASP* 1.3 80.2 - - - +
110B GLY* 1.3 60.9 + - - +
111B GLU* 3.4 27.7 + - + +
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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