Contacts of the strand formed by residues 112 - 123 (chain B) in PDB entry 2Y1Z
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A MET* 4.7 3.8 - - - -
121A LYS 3.3 7.9 - - - -
122A TYR* 4.3 11.7 - - - -
106B GLU 3.9 0.8 - - - +
107B ARG* 3.7 0.9 - - - +
108B GLN* 2.8 46.9 + - - +
111B HIS* 1.3 75.6 - - - +
113B PHE* 1.3 61.0 + - - +
1152B MRD 3.5 4.6 - - - +
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Residues in contact with PHE 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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119A HIS* 4.3 14.6 - + + -
120A GLY* 3.0 5.2 - - - -
121A LYS* 2.7 57.9 + - + +
122A TYR* 4.4 6.4 - - - -
105B GLU* 4.6 21.3 - - + -
106B GLU 3.4 9.4 - - - -
107B ARG* 4.3 20.4 - - + -
112B GLY* 1.3 74.6 - - - +
114B ILE* 1.3 66.0 + - - +
115B SER* 3.7 31.2 - - - -
1152B MRD 4.1 18.8 - - + +
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Residues in contact with ILE 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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79A LEU* 3.8 28.3 - - + -
118A PHE* 3.9 16.4 - - + -
119A HIS 3.4 15.0 - - - +
120A GLY* 4.4 2.2 - - - -
122A TYR* 3.9 13.5 - - + +
104B HIS* 3.9 5.6 + - + +
105B GLU* 3.4 3.5 - - - +
106B GLU* 2.9 67.1 + - + +
113B PHE* 1.3 76.6 - - - +
115B SER* 1.3 61.6 + - - +
116B ARG* 4.1 23.6 - - + -
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Residues in contact with SER 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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118A PHE* 3.0 7.8 - - - +
119A HIS* 2.7 54.5 + - - -
103B LYS* 5.2 4.5 - - - +
104B HIS 3.4 4.5 - - - -
105B GLU* 3.8 18.9 + - - +
113B PHE* 3.7 27.8 - - - -
114B ILE* 1.3 75.1 - - - +
116B ARG* 1.3 65.8 + - - +
117B GLU* 5.5 4.2 + - - +
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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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79A LEU* 5.9 3.2 - - - +
80A ASP 3.6 22.2 + - - -
84A PHE* 5.4 5.6 - - - -
116A ARG* 4.0 21.8 - - - +
117A GLU 3.6 3.6 - - - +
118A PHE* 3.9 21.7 - - + +
81B VAL 6.2 0.2 - - - -
82B LYS 6.1 0.2 - - - +
83B HIS* 3.3 48.1 - - - +
84B PHE* 3.6 24.2 - - + -
103B LYS* 3.3 4.7 - - - +
104B HIS* 2.7 57.5 + - + +
114B ILE* 4.1 17.6 - - + +
115B SER* 1.3 79.4 + - - +
117B GLU* 1.3 62.5 + - - +
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Residues in contact with GLU 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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115A SER 4.1 0.4 - - - +
116A ARG* 3.5 1.0 - - - +
117A GLU* 2.8 60.1 + - + +
119A HIS* 5.5 4.0 + - + +
84B PHE* 4.2 3.2 - - - -
101B HIS* 3.2 23.9 + - + +
102B GLY 3.3 12.8 - - - +
103B LYS* 4.5 21.3 - - + +
115B SER* 5.5 4.5 + - - +
116B ARG* 1.3 76.9 - - - +
118B PHE* 1.3 68.5 + - - +
119B HIS* 5.8 1.5 - - + +
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Residues in contact with PHE 118 (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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114A ILE* 4.2 16.4 - - + -
115A SER 3.2 11.2 - - - +
116A ARG* 3.7 24.2 - - + +
79B LEU* 4.5 7.9 - - + -
80B ASP 6.0 0.2 - - - -
81B VAL* 3.6 29.6 - - + -
84B PHE* 3.5 22.9 - + + -
89B LEU* 3.6 19.1 - - + -
100B VAL* 4.1 23.3 - - + -
101B HIS* 3.2 26.1 - - - -
102B GLY* 3.1 45.9 + - - -
117B GLU* 1.3 77.2 - - - +
119B HIS* 1.3 64.4 + - - +
143B LEU* 4.7 4.9 - - + -
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Residues in contact with HIS 119 (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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113A PHE* 3.8 26.2 - + - -
114A ILE* 3.3 4.7 - - - -
115A SER* 2.9 43.2 + - - +
99B GLU* 3.2 38.9 + - + -
100B VAL* 3.4 14.3 + - - -
101B HIS* 4.2 16.6 - + + +
117B GLU* 5.8 2.0 - - + +
118B PHE* 1.3 77.7 - - - +
120B GLY* 1.3 60.8 + - - +
121B LYS* 4.2 8.4 - - + -
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Residues in contact with GLY 120 (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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113A PHE* 3.2 18.2 - - - -
114A ILE* 4.2 4.5 - - - -
99B GLU* 3.4 1.2 - - - +
100B VAL* 2.8 51.1 + - - +
119B HIS* 1.3 77.4 - - - +
121B LYS* 1.3 68.4 + - - +
122B TYR* 4.5 2.7 - - - -
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Residues in contact with LYS 121 (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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112A GLY* 3.1 4.0 - - - -
113A PHE* 3.0 55.9 + - + -
1153A MPD 4.2 14.5 - - + +
94B LEU* 4.9 8.6 - - - +
97B VAL* 4.2 15.7 - - + +
98B ILE 3.0 9.0 - - - +
99B GLU* 3.6 36.8 + - + -
119B HIS* 4.2 10.5 - - + -
120B GLY* 1.3 79.7 - - - +
122B TYR* 1.3 66.0 + - - +
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Residues in contact with TYR 122 (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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111A HIS 3.2 12.3 - - - +
112A GLY* 4.4 7.4 - - - -
113A PHE 4.1 4.5 - - - -
1153A MPD 4.2 6.1 - - - -
66B MET* 2.9 42.1 - - + +
68B MET* 4.3 16.2 - - + -
75B PHE* 5.5 0.4 - - + -
77B VAL* 3.8 30.1 - - + -
79B LEU* 3.1 28.2 - - + +
97B VAL* 3.4 2.8 - - - -
98B ILE* 2.8 65.1 + - + +
100B VAL* 3.1 24.5 - - + +
120B GLY 4.5 0.2 - - - -
121B LYS* 1.3 85.4 - - - +
123B ARG* 1.3 64.2 + - - +
145B VAL* 5.5 1.8 - - + -
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Residues in contact with ARG 123 (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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110A GLU* 3.6 31.7 + - - +
111A HIS* 3.0 46.5 + - + +
1153A MPD 4.1 7.1 - - + +
68B MET* 4.7 1.9 - - - +
75B PHE* 4.2 11.1 - - - -
96B ASP* 3.7 22.7 - - - +
97B VAL* 4.5 8.5 - - + +
122B TYR* 1.3 76.1 - - - +
124B ILE* 1.3 70.4 + - - +
125B PRO* 3.5 10.7 - - - +
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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