Contacts of the strand formed by residues 112 - 123 (chain R) in PDB entry 2YGD
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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121O LYS 4.2 6.5 - - - -
122O TYR* 5.1 3.8 - - - -
123O ARG 5.9 0.2 - - - -
108R GLN* 3.6 4.7 - - - +
109R ASP* 2.8 42.2 + - - +
110R GLU 3.6 0.4 - - - -
111R HIS* 1.3 78.0 - - - +
113R PHE* 1.3 75.2 + - - -
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Residues in contact with PHE 113 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120O ARG* 3.6 5.9 - - - +
121O LYS* 3.3 64.6 + - + +
122O TYR* 5.2 1.4 - - - -
105R GLU* 3.4 28.5 - - + +
107R ARG 4.0 3.1 - - - -
108R GLN* 3.7 30.5 - - + -
112R GLY* 1.3 84.6 - - - -
114R ILE* 1.3 63.7 + - - +
115R SER 3.7 1.7 + - - -
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Residues in contact with ILE 114 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80O ASP* 3.4 20.9 - - - +
118O PHE* 5.4 5.2 - - + -
120O ARG* 3.4 48.0 - - + +
105R GLU* 3.3 4.7 - - - +
106R GLU* 2.8 38.2 + - + +
107R ARG* 2.9 62.5 + - + +
108R GLN 5.2 0.7 - - - +
109R ASP* 5.0 10.5 - - + -
113R PHE* 1.3 73.6 - - - +
115R SER* 1.3 59.3 + - - +
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Residues in contact with SER 115 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118O PHE* 3.5 11.7 - - - -
119O HIS* 2.9 53.8 + - - -
120O ARG* 4.2 0.9 + - - +
121O LYS* 2.9 24.9 + - - -
104R HIS 3.3 10.3 - - - -
105R GLU* 4.1 3.0 - - - +
113R PHE 3.7 0.4 + - - -
114R ILE* 1.3 75.5 - - - +
116R ARG* 1.3 59.4 + - - +
117R GLU* 3.6 23.6 + - - -
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Residues in contact with ARG 116 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82O LYS* 4.1 13.2 - - - +
116O ARG* 4.7 7.1 - - - +
117O GLU 3.6 8.7 - - - +
118O PHE* 3.2 37.9 - - + -
83R HIS* 2.9 45.2 + - - +
84R PHE* 3.2 32.0 - - + +
104R HIS* 2.9 29.5 + - + +
105R GLU* 4.5 0.2 - - - +
106R GLU* 2.7 45.2 + - + -
114R ILE 3.7 1.6 + - - -
115R SER* 1.3 74.3 - - - +
117R GLU* 1.3 63.2 + - - +
118R PHE* 3.7 15.9 - - + -
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Residues in contact with GLU 117 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116O ARG* 3.4 2.4 - - - +
117O GLU* 2.7 48.4 + - + +
119O HIS* 4.0 17.1 + - + +
101R HIS* 2.7 35.1 + - - +
102R GLY 3.1 11.0 - - - +
103R LYS* 3.5 16.1 - - - +
104R HIS 4.2 3.1 - - - +
115R SER* 3.6 19.8 + - - -
116R ARG* 1.3 87.6 - - - +
118R PHE* 1.3 71.2 + - - +
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Residues in contact with PHE 118 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O GLU* 3.5 25.4 - - + -
107O ARG* 5.9 4.3 - - - -
114O ILE* 5.2 6.7 - - + -
115O SER 3.3 16.8 - - - +
116O ARG* 3.5 25.6 - - + +
117O GLU* 4.5 2.7 - - - +
81R VAL* 3.7 33.0 - - + -
82R LYS 5.4 1.6 - - - -
83R HIS* 3.2 34.3 - + + -
84R PHE* 3.6 30.7 - + - -
100R VAL 3.8 0.2 - - - +
101R HIS* 3.3 9.1 - - - -
102R GLY 2.8 32.3 + - - +
116R ARG* 3.7 12.6 - - + -
117R GLU* 1.3 88.6 - - - +
119R HIS* 1.3 61.1 + - - +
120R ARG* 3.9 2.0 - - + +
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Residues in contact with HIS 119 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O PHE 3.7 0.2 - - - +
115O SER* 2.8 29.5 + - - -
116O ARG 5.4 0.2 - - - -
117O GLU* 4.2 17.0 + - - +
99R GLU* 2.7 33.6 + - + -
100R VAL 3.5 11.9 - - - -
101R HIS* 5.4 7.6 - - + -
118R PHE* 1.3 72.5 - - - +
120R ARG* 1.3 58.2 + - - +
121R LYS* 2.8 51.0 + - + +
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Residues in contact with ARG 120 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O ARG* 3.3 17.2 - - - +
109O ASP* 4.4 1.2 + - - -
113O PHE 4.0 3.1 - - - -
114O ILE* 3.4 40.2 - - + +
115O SER 5.3 0.7 - - - +
78R ASN* 2.9 20.2 + - - +
79R LEU* 3.5 25.7 - - + +
80R ASP* 2.7 66.5 + - - +
81R VAL* 4.0 9.2 - - + +
99R GLU* 3.4 0.7 - - - +
100R VAL* 2.7 50.1 + - + +
118R PHE* 3.9 0.8 - - + -
119R HIS* 1.3 72.9 - - - +
121R LYS* 1.3 65.0 + - - +
122R TYR* 3.0 18.1 + - + -
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Residues in contact with LYS 121 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O GLY* 3.2 3.6 - - - -
113O PHE* 3.1 58.3 + - + +
114O ILE* 5.4 0.2 - - - +
115O SER* 2.9 20.3 + - - -
79R LEU* 3.7 2.4 - - - +
98R ILE 3.3 6.3 - - - -
99R GLU* 3.5 34.1 - - + +
119R HIS* 2.8 48.3 + - + +
120R ARG* 1.3 82.4 - - - +
122R TYR* 1.3 68.7 + - - +
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Residues in contact with TYR 122 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O ASP* 2.6 40.0 + - - -
110O GLU* 5.1 5.2 - - + -
111O HIS 3.5 9.9 - - - +
112O GLY* 3.5 15.7 - - - -
114O ILE* 4.5 1.4 - - + +
77R VAL* 3.8 27.1 - - + -
78R ASN 3.3 20.2 + - - -
79R LEU* 3.7 19.3 - - + -
97R VAL* 3.4 4.6 - - - +
98R ILE* 2.9 37.2 + - + +
120R ARG* 3.0 27.2 + - + -
121R LYS* 1.3 79.6 - - - +
123R ARG* 1.3 57.6 + - - +
124R ILE* 3.5 27.4 + - + -
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Residues in contact with ARG 123 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O HIS* 3.0 37.5 + - + +
96R ASP* 2.7 33.4 + - - +
97R VAL* 3.6 20.0 - - + +
122R TYR* 1.3 70.8 - - - +
124R ILE* 1.3 58.8 + - - +
125R PRO* 3.7 10.0 - - + +
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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