Contacts of the helix formed by residues 109 - 117 (chain B) in PDB entry 5IYB
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 MET 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B PRO* 4.5 23.1 - - + +
108B MET* 1.3 87.3 - - - +
110B PRO* 1.3 63.5 - - + +
111B ASN* 3.1 4.0 - - + +
112B GLU* 2.7 45.4 + - + +
113B ALA* 3.1 8.0 + - - +
120B TYR* 4.5 1.1 - - - -
162B LEU* 3.9 19.5 - - + -
174B LEU* 3.6 46.7 - - + +
41L TYR* 6.5 0.7 - - + -
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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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108B MET 4.5 0.4 - - - +
109B MET* 1.3 85.4 - - + +
111B ASN* 1.3 61.1 + - - +
113B ALA* 3.3 15.3 + - + +
114B ARG* 3.4 19.0 + - - +
120B TYR* 3.8 31.1 - - + -
156B LEU* 4.0 23.6 - - + -
163B LEU* 3.4 45.5 - - + -
174B LEU* 4.6 4.0 - - + -
176B GLU* 4.5 11.4 - - + +
186B ILE* 4.1 2.7 - - + +
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Residues in contact with ASN 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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109B MET* 2.9 3.1 + - + -
110B PRO* 1.3 79.0 - - + +
112B GLU* 1.3 65.6 + - - +
113B ALA 3.1 1.6 - - - -
114B ARG* 3.1 38.2 + - - +
115B LEU* 3.2 24.2 + - - +
174B LEU 5.0 7.6 - - - +
175B ASN* 4.2 18.1 + - - +
176B GLU* 4.0 7.0 - - + +
739B ASN* 4.4 7.3 + - - -
742B VAL* 3.9 31.6 + - - +
743B ARG* 4.5 6.4 - - - +
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Residues in contact with GLU 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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98B HIS* 5.4 1.8 - - - -
107B PRO 5.5 2.3 - - - +
108B MET* 5.2 4.4 - - + -
109B MET* 2.7 33.3 + - + +
111B ASN* 1.3 74.8 - - - +
113B ALA* 1.3 62.5 + - - +
115B LEU* 3.4 5.3 + - - -
116B ARG* 3.2 62.1 + - + +
118B LEU* 4.8 7.7 - - + +
41L TYR* 4.4 23.0 - - - -
42L ARG* 3.9 10.6 + - - +
43L ILE* 5.3 14.5 - - + +
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Residues in contact with ALA 113 (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 MET* 3.9 22.4 - - - -
109B MET 3.1 5.2 + - - +
110B PRO* 3.3 18.2 - - + +
111B ASN 3.1 0.8 - - - -
112B GLU* 1.3 77.8 - - - +
114B ARG* 1.3 56.8 + - - +
117B ASN* 3.2 7.6 + - - -
118B LEU* 2.9 40.3 + - + +
120B TYR* 4.3 19.5 - - + +
186B ILE* 4.6 7.2 - - + -
189B GLY* 4.0 3.8 - - - -
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Residues in contact with ARG 114 (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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110B PRO 3.4 8.6 + - - +
111B ASN* 3.1 33.1 + - - +
113B ALA* 1.3 75.7 - - - +
115B LEU* 1.3 65.6 + - + +
117B ASN* 3.5 9.0 + - - +
156B LEU* 3.9 8.3 - - - +
176B GLU* 2.6 42.0 + - - -
184B TYR* 3.9 0.4 + - - -
186B ILE* 3.4 34.4 - - + +
189B GLY* 4.1 20.3 - - - +
191B GLU* 3.6 30.7 + - - -
739B ASN* 5.2 0.8 - - - +
743B ARG* 4.0 25.0 - - - +
920B LYS* 3.3 18.2 + - - -
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Residues in contact with LEU 115 (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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111B ASN* 3.2 28.4 + - - +
112B GLU* 3.4 3.8 + - - +
114B ARG* 1.3 78.4 - - + +
116B ARG* 1.3 61.3 + - - +
117B ASN 3.3 0.2 - - - -
742B VAL* 4.0 21.1 - - + +
743B ARG* 5.1 0.2 - - - -
744B MET* 3.8 45.8 - - + +
908B MET* 3.5 37.4 - - - +
918B PHE* 3.9 2.6 - - - -
920B LYS* 3.5 13.5 - - + +
43L ILE* 4.0 28.7 - - + -
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Residues in contact with ARG 116 (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 HIS* 3.9 16.3 + - - -
100B GLU* 3.6 15.8 + - - -
112B GLU* 3.2 37.4 + - - +
115B LEU* 1.3 76.6 - - - +
117B ASN* 1.3 68.8 + - - +
118B LEU* 3.8 20.4 - - + +
910B THR* 3.5 19.0 + - + +
911B LEU* 2.8 43.1 + - - +
912B ASN* 3.2 23.9 + - - +
913B GLN 3.9 0.3 + - - -
918B PHE* 4.5 2.0 - - - -
42L ARG* 2.9 40.8 - - - +
43L ILE* 3.4 29.2 - - + -
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Residues in contact with ASN 117 (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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113B ALA 3.2 8.7 + - - -
114B ARG 3.5 0.5 + - - +
115B LEU 3.3 1.6 - - - -
116B ARG* 1.3 82.2 - - - +
118B LEU* 1.3 68.6 + - - +
188B ASN* 3.6 19.9 + - - +
189B GLY* 3.2 20.0 - - - -
815B LYS* 4.5 15.2 - - - +
912B ASN* 4.7 6.0 - - + +
913B GLN* 3.8 13.0 + - - +
918B PHE* 3.1 31.7 - - + -
920B LYS* 3.4 18.5 + - - +
59Y G 5.3 6.1 + - - -
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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