Contacts of the strand formed by residues 112 - 123 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A GLN* 3.0 31.4 + - - -
109A ASP 3.5 5.5 + - - +
110A GLU 3.6 2.6 - - - +
111A HIS* 1.3 82.0 + - - +
113A PHE* 1.3 61.5 + - - +
1153A MPD 3.5 15.0 - - - +
68B MET* 5.2 3.6 - - - -
121B LYS 3.1 13.0 - - - -
122B TYR* 4.1 7.2 - - - -
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLU* 6.5 0.7 - - - -
106A GLU 3.3 8.1 - - - -
107A ARG* 3.9 16.4 - - + -
108A GLN* 5.1 1.3 + - - -
112A GLY* 1.3 74.3 - - - +
114A ILE* 1.3 70.4 + - - +
115A SER* 4.7 8.1 - - - -
1153A MPD 3.7 26.2 - - + -
66B MET* 4.6 2.5 - - - -
119B HIS* 3.8 41.3 - + - -
120B GLY* 3.2 3.1 - - - -
121B LYS* 3.0 65.2 + - + +
122B TYR* 4.1 6.0 - - - -
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Residues in contact with ILE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 3.9 1.9 + - + +
105A GLU* 3.3 3.2 - - - +
106A GLU* 2.8 63.5 + - + +
113A PHE* 1.3 81.6 - - - +
115A SER* 1.3 71.0 + - - +
116A ARG* 4.2 22.7 - - + +
65B ALA* 5.7 2.0 - - + -
66B MET* 3.4 20.6 - - + -
79B LEU* 3.4 32.8 - - + -
118B PHE* 4.2 16.4 - - + -
119B HIS 3.3 15.9 - - - +
120B GLY* 4.5 0.9 - - - -
122B TYR* 4.7 1.8 - - - +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LYS* 5.5 4.5 - - - -
104A HIS 3.4 3.6 - - - -
105A GLU* 3.5 28.9 - - - -
113A PHE* 4.4 9.6 - - - -
114A ILE* 1.3 75.1 - - - +
116A ARG* 1.3 63.7 + - - +
117A GLU* 5.7 0.2 - - - +
117B GLU 4.1 0.2 - - - +
118B PHE* 3.2 4.0 - - - +
119B HIS* 2.9 46.4 + - - +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A HIS* 3.3 37.2 - - - +
84A PHE* 4.0 22.9 - - + -
103A LYS* 3.4 6.4 - - - +
104A HIS* 2.8 47.3 + - + +
114A ILE* 4.4 19.3 - - + +
115A SER* 1.3 77.2 - - - +
117A GLU* 1.3 62.2 + - - +
65B ALA* 3.7 21.0 - - - +
79B LEU* 5.9 0.6 - - - +
80B ASP* 2.9 29.3 + - - -
84B PHE* 5.7 3.3 - - - -
116B ARG* 4.0 21.0 - - - +
117B GLU 3.5 4.7 - - - +
118B PHE* 3.7 24.5 - - + +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A PHE* 4.1 3.0 - - - -
101A HIS* 3.1 23.8 + - - +
102A GLY 3.2 14.6 - - - +
103A LYS* 4.4 21.9 + - + +
115A SER 5.6 0.4 - - - -
116A ARG* 1.3 76.4 - - - +
118A PHE* 1.3 64.6 + - - +
119A HIS* 3.4 22.5 + - + +
116B ARG* 3.6 0.5 - - - +
117B GLU* 2.8 60.3 + - + +
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Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A LEU* 4.0 16.2 - - + -
81A VAL* 3.6 31.6 - - + -
84A PHE* 4.0 17.9 - + + -
89A LEU* 3.8 12.1 - - + -
100A VAL* 3.7 30.1 - - + -
101A HIS* 3.1 10.3 - - - -
102A GLY* 3.1 55.2 + - - -
117A GLU* 1.3 76.6 - - - +
119A HIS* 1.3 68.8 + - - +
143A LEU* 4.9 1.3 - - + -
114B ILE* 3.9 16.2 - - + -
115B SER 3.0 13.7 - - - +
116B ARG* 3.9 23.3 - - + +
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Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL 3.3 6.5 - - - +
101A HIS* 3.0 35.6 - + + +
117A GLU* 3.4 30.9 + - + +
118A PHE* 1.3 77.9 - - - +
120A GLY* 1.3 57.2 + - - +
121A LYS* 6.5 1.1 - - - -
113B PHE* 3.9 11.4 - + + +
114B ILE* 3.4 2.6 - - - +
115B SER* 2.7 59.1 + - - +
117B GLU* 5.5 4.7 + - + +
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Residues in contact with GLY 120 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A ILE 3.6 0.3 - - - +
99A GLU* 3.4 5.0 - - - +
100A VAL* 2.8 54.3 + - - +
119A HIS* 1.3 75.9 - - - +
121A LYS* 1.3 64.3 + - - +
122A TYR* 4.2 7.1 - - - -
113B PHE* 3.0 11.4 - - - -
114B ILE* 4.3 5.2 - - - -
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Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A VAL* 4.2 11.4 - - + -
98A ILE 3.1 8.3 - - - +
99A GLU* 4.0 27.1 - - + -
119A HIS* 6.5 1.6 - - - -
120A GLY* 1.3 78.0 - - - +
122A TYR* 1.3 64.2 + - - +
111B HIS 4.0 0.4 - - - +
112B GLY* 3.3 4.3 - - - -
113B PHE* 2.7 56.3 + - + +
1152B MRD 3.7 24.4 - - - +
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLU 4.4 13.3 + - - -
68A MET* 4.1 31.2 - - + -
75A PHE* 5.3 0.4 - - + -
77A VAL* 3.5 42.4 - - + -
79A LEU* 3.8 20.6 - - + +
97A VAL* 4.4 2.7 - - - +
98A ILE* 2.8 57.5 + - + +
100A VAL* 4.3 12.8 - - + -
120A GLY* 4.2 15.5 - - - -
121A LYS* 1.3 80.9 - - - +
123A ARG* 1.3 62.4 + - - +
124A ILE* 3.5 1.0 + - - +
111B HIS 3.5 2.9 - - - -
112B GLY* 4.3 5.4 - - - -
113B PHE 4.4 11.7 - - - -
114B ILE* 3.9 19.1 - - + +
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Residues in contact with ARG 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A MET* 3.8 14.7 - - - -
75A PHE* 4.3 2.5 - - - -
96A ASP* 3.2 34.6 + - - +
97A VAL* 4.5 5.8 - - + -
122A TYR* 1.3 72.3 - - - +
124A ILE* 1.3 70.0 + - - +
125A PRO* 3.7 6.2 - - - -
110B GLU* 3.4 29.0 + - - +
111B HIS* 2.9 38.5 + - + +
1152B MRD 3.8 16.7 - - + +
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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