Contacts of the helix formed by residues 101 - 111 (chain B) in PDB entry 4IA4
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B ILE* 6.1 1.3 - - + -
99B HIS* 2.8 6.5 + - - +
100B ILE* 1.3 80.7 - - - +
102B PRO* 1.3 66.8 - - - +
103B ALA* 2.9 23.3 + - - +
104B VAL* 2.8 41.4 + - + +
105B THR* 2.9 13.5 + - - -
126B GLN* 3.1 5.4 - - - +
175B LEU* 3.6 14.7 - - + +
206B VAL* 6.2 0.2 - - - +
221B ILE 2.8 21.0 + - - -
222B ASN* 2.8 28.3 - - - +
223B PRO* 3.5 4.7 - - - +
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Residues in contact with PRO 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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101B ASN* 1.3 88.1 - - - +
103B ALA* 1.3 56.7 + - - +
105B THR* 3.3 3.7 + - - +
106B PHE* 2.9 30.9 + - - +
123B MET* 3.7 24.0 - - + +
126B GLN* 2.7 20.4 - - + +
127B CYS* 5.2 3.1 - - - -
222B ASN* 3.9 1.3 - - - +
223B PRO* 3.9 15.3 - - + -
224B ALA* 3.2 45.3 - - + +
246B TRP* 5.5 2.5 - - + -
250B PHE* 4.5 11.7 - - + -
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Residues in contact with ALA 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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101B ASN* 2.9 13.8 + - - +
102B PRO* 1.3 77.2 - - - +
104B VAL* 1.3 63.1 + - - +
106B PHE* 4.2 5.8 - - - -
107B GLY* 3.2 17.8 + - - -
172B THR* 4.1 16.8 - - + -
176B VAL* 4.1 2.5 - - + +
222B ASN 5.6 0.4 - - - +
223B PRO* 3.8 3.9 - - + +
249B PRO* 3.8 37.2 - - + +
250B PHE* 4.4 4.0 - - - +
253B ALA* 3.2 13.9 - - - +
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Residues in contact with VAL 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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99B HIS* 4.3 27.8 - - + +
101B ASN* 2.8 28.3 + - + +
103B ALA* 1.3 74.5 - - - +
105B THR* 1.3 68.3 + - - +
107B GLY* 3.5 1.6 + - - -
108B LEU* 3.4 20.9 + - + +
175B LEU* 3.8 25.6 - - + -
176B VAL* 4.5 10.4 - - + +
179B VAL* 3.6 40.2 - - + -
197B LEU* 4.9 1.8 - - + -
202B ILE* 6.5 0.2 - - + -
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Residues in contact with THR 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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99B HIS* 3.0 30.7 + - + +
101B ASN 2.9 11.5 + - - -
102B PRO* 3.6 8.5 - - - -
104B VAL* 1.3 76.5 - - - +
106B PHE* 1.3 65.9 + - - +
108B LEU* 3.0 6.9 + - - +
109B PHE* 2.8 20.8 + - - +
114B VAL* 4.4 6.4 - - + +
119B ALA* 3.9 37.0 - - + +
122B TYR* 4.0 10.9 - - + +
123B MET* 4.3 5.6 - - + -
126B GLN* 3.4 16.3 + - - -
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Residues in contact with PHE 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 PRO 2.9 18.4 + - - +
103B ALA* 3.9 4.0 - - - +
105B THR* 1.3 75.8 - - - +
107B GLY* 1.3 62.5 + - - +
109B PHE* 3.1 22.0 + + - +
110B LEU* 2.9 65.3 + - + +
123B MET* 3.8 11.8 - - + +
250B PHE* 3.3 63.9 - + + -
253B ALA* 4.3 5.4 - - + -
254B ALA* 4.3 4.3 - - + -
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Residues in contact with GLY 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 ALA 3.2 14.9 + - - -
104B VAL 4.0 1.6 - - - -
105B THR 3.2 0.2 - - - -
106B PHE* 1.3 80.0 - - - +
108B LEU* 1.3 60.0 + - - +
110B LEU* 3.3 12.1 + - - +
111B ALA 3.2 13.9 + - - -
176B VAL* 4.5 5.6 - - - -
180B PHE* 3.3 16.4 - - - -
253B ALA* 4.2 22.7 - - - -
257B ALA* 3.6 2.1 - - - +
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Residues in contact with LEU 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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99B HIS* 3.6 30.7 - - + +
104B VAL 3.4 11.5 + - - +
105B THR 3.0 7.2 + - - +
107B GLY* 1.3 73.0 - - - +
109B PHE* 1.3 61.8 + - - +
111B ALA* 2.8 18.9 + - - +
112B ARG 2.9 9.5 + - - -
113B LYS* 3.1 29.7 + - + -
114B VAL* 4.1 14.6 - - + -
176B VAL* 6.0 0.2 - - + -
179B VAL* 4.1 21.8 - - + -
180B PHE* 3.2 32.8 - - + -
183B THR* 4.4 11.2 - - + -
194B VAL* 5.5 2.5 - - + -
195B PRO* 5.7 4.0 - - + -
197B LEU* 4.9 6.3 - - + -
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Residues in contact with PHE 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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26B PHE* 3.7 26.5 - + - -
105B THR 2.8 12.6 + - - +
106B PHE* 3.1 31.0 - + - +
108B LEU* 1.3 77.3 - - - +
110B LEU* 1.3 74.0 + - + +
112B ARG* 2.7 28.9 + - - +
114B VAL* 3.4 25.9 - - + +
115B SER 4.3 0.7 - - - -
116B LEU* 3.8 36.8 - - + -
119B ALA* 4.5 14.6 - - + -
123B MET* 5.9 0.4 - - + -
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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 PHE* 2.9 59.7 + - + +
107B GLY* 3.5 9.4 - - - +
109B PHE* 1.3 91.8 - - + +
111B ALA* 1.3 58.4 + - - +
112B ARG* 3.1 9.7 + - - +
254B ALA* 3.8 25.1 - - + -
257B ALA* 4.5 8.7 - - + -
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Residues in contact with ALA 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 GLY 3.2 5.3 + - - +
108B LEU* 2.8 11.3 + - - +
110B LEU* 1.3 75.8 - - - +
112B ARG* 1.3 70.1 + - - +
113B LYS* 3.5 14.4 + - + +
180B PHE* 3.6 30.7 - - + -
257B ALA* 5.1 1.1 - - + -
261B GLN* 3.2 32.5 - - + +
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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