Contacts of the helix formed by residues 95 - 108 (chain B) in PDB entry 2YZ2
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 ARG 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ALA* 3.7 6.5 - - - +
94B GLU* 1.3 82.4 - - + +
96B VAL* 1.3 67.2 + - - +
97B PHE* 3.0 34.0 + - - +
98B ASP* 3.2 41.9 + - - +
99B GLU* 3.3 9.0 + - - +
132B LYS* 3.4 20.5 + - - +
133B ASP* 3.0 36.2 + - - +
134B ARG 3.2 6.1 - - - +
136B PRO* 3.7 4.5 - - - -
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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 ARG* 1.3 70.8 - - - +
97B PHE* 1.3 63.9 + - - +
99B GLU* 3.1 4.8 + - - -
100B VAL* 3.1 28.8 + - + +
121B MET* 3.6 29.8 - - + -
131B PHE* 3.2 24.5 - - + +
134B ARG* 2.9 19.7 + - + +
136B PRO* 3.5 12.7 - - + +
139B LEU* 3.4 32.8 - - + -
147B VAL* 3.9 20.0 - - + -
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Residues in contact with PHE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG* 3.0 29.7 + - - +
96B VAL* 1.3 76.5 - - - +
98B ASP* 1.3 72.3 + - - +
100B VAL* 3.6 2.4 + - - +
101B ALA* 2.9 35.6 + - + +
105B LYS* 4.5 12.8 - - - -
113B PRO* 4.7 6.3 - - + -
114B VAL* 4.2 26.2 - - + -
117B VAL* 3.8 38.0 - - + +
121B MET* 5.2 0.2 - - - -
128B PHE* 4.1 23.6 - + - -
132B LYS* 2.8 29.1 + - + +
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Residues in contact with ASP 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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92B PHE* 3.7 13.4 - - + -
93B ALA* 3.7 19.4 - - + +
94B GLU* 5.2 1.2 + - - +
95B ARG* 3.2 37.9 + - - +
97B PHE* 1.3 88.0 - - - +
99B GLU* 1.3 65.0 + - - +
101B ALA* 4.1 3.8 - - - +
102B PHE* 3.1 19.2 + - - +
105B LYS* 4.7 8.8 + - - -
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Residues in contact with GLU 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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90B GLN 4.2 2.3 - - - +
91B PHE* 3.5 42.5 - - + +
92B PHE* 2.8 24.4 + - - -
93B ALA* 2.8 34.8 + - + +
95B ARG 3.3 8.7 + - - +
96B VAL* 3.1 13.8 + - - +
98B ASP* 1.3 80.5 - - - +
100B VAL* 1.3 61.8 + - - +
102B PHE* 3.6 11.3 + - - +
103B ALA 5.2 0.2 + - - -
136B PRO* 4.4 5.4 - - + -
147B VAL* 4.0 14.6 - - + -
151B SER* 3.5 19.9 + - - -
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Residues in contact with VAL 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B VAL* 3.1 29.9 + - + +
97B PHE 4.0 2.9 - - - +
99B GLU* 1.3 76.4 - - - +
101B ALA* 1.3 62.2 + - - +
102B PHE 3.4 0.7 + - - -
103B ALA 4.3 0.7 + - - -
117B VAL* 4.0 20.6 - - + -
120B ALA* 4.2 6.5 - - + -
121B MET* 4.4 7.6 - - + -
126B LEU* 6.0 0.2 - - + -
147B VAL* 4.1 15.3 - - + +
150B ALA* 3.8 41.3 - - + +
151B SER* 3.9 6.6 - - - -
154B VAL* 3.2 29.3 - - + +
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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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97B PHE* 2.9 36.1 + - + +
98B ASP* 3.3 5.5 + - - +
100B VAL* 1.3 77.0 - - - +
102B PHE* 1.3 66.8 + - - +
103B ALA 3.4 0.2 - - - -
104B VAL* 3.1 21.5 - - - +
105B LYS* 3.1 24.3 + - + +
113B PRO* 4.6 3.8 - - + -
117B VAL* 3.6 20.6 - - + -
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Residues in contact with PHE 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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92B PHE* 3.6 42.6 - + + -
98B ASP 3.1 9.7 + - - +
99B GLU 3.9 5.8 - - - +
100B VAL 3.3 2.4 - - - -
101B ALA* 1.3 75.8 - - - +
103B ALA* 1.3 64.0 + - + +
105B LYS* 3.3 7.7 + - + +
106B ASN* 2.8 55.0 + - + +
107B PHE* 6.5 0.2 - + - -
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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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99B GLU 5.2 0.2 + - - -
100B VAL 4.3 1.4 + - - -
101B ALA 3.2 0.8 + - - -
102B PHE* 1.3 87.6 - - + +
104B VAL* 1.3 52.8 + - - +
106B ASN* 3.7 2.6 - - - -
107B PHE* 2.7 50.6 + - + +
151B SER* 3.8 16.9 + - - +
154B VAL* 3.9 2.7 - - + -
155B HIS* 3.6 29.8 - - + +
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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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101B ALA* 3.1 19.5 - - - +
103B ALA* 1.3 73.8 - - - +
105B LYS* 1.3 59.3 + - - +
107B PHE* 4.6 0.2 - - - -
108B TYR* 2.7 47.4 + - + +
111B ARG 5.7 1.8 - - - +
113B PRO* 4.1 27.4 - - + -
116B LEU* 4.2 17.7 - - + -
117B VAL* 4.8 0.7 - - + -
154B VAL* 3.6 27.8 - - + +
155B HIS* 3.3 36.3 - - + +
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Residues in contact with LYS 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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97B PHE* 4.5 13.4 - - - -
98B ASP* 4.7 9.0 + - - -
101B ALA* 3.1 30.6 + - + +
102B PHE* 3.7 7.0 - - + +
104B VAL* 1.3 78.0 - - - +
106B ASN* 1.3 62.9 + - - +
108B TYR 4.8 0.2 - - - -
109B PRO* 3.6 24.9 - - - +
111B ARG 6.2 0.2 - - - -
113B PRO* 4.0 32.1 - - + -
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Residues in contact with ASN 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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77B ARG* 4.9 5.9 - - - +
78B ARG* 4.7 5.4 + - - -
102B PHE* 2.8 44.0 + - + +
103B ALA* 4.0 2.5 - - - +
105B LYS* 1.3 79.7 - - - +
107B PHE* 1.3 92.9 + - + +
108B TYR 3.8 0.2 + - - -
109B PRO* 3.9 8.0 - - - +
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Residues in contact with PHE 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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77B ARG* 3.6 55.0 - - + -
78B ARG* 2.6 56.4 + - + +
80B ILE 4.3 1.8 - - - -
102B PHE* 6.5 0.2 - + - -
103B ALA* 2.7 30.0 + - + +
104B VAL* 4.6 0.2 - - - -
106B ASN* 1.3 97.0 - - + +
108B TYR* 1.3 73.2 + - + +
109B PRO* 3.6 5.3 - - - +
155B HIS* 3.3 42.8 - + - -
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Residues in contact with TYR 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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78B ARG* 3.7 38.2 + - + +
79B ASN* 4.8 6.2 + - - -
104B VAL* 2.7 28.3 + - + +
105B LYS* 4.8 0.2 - - - -
107B PHE* 1.3 87.7 - - + +
109B PRO* 1.3 64.9 - - - +
110B ASP* 3.0 13.3 + - - +
111B ARG* 3.1 78.9 + - + +
116B LEU* 6.0 1.1 - - + -
155B HIS* 3.7 35.4 + - + -
156B GLU 5.8 0.2 + - - -
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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