Contacts of the strand formed by residues 112 - 123 (chain A) in PDB entry 2XYA
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 THR 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A MET* 4.4 1.1 - - - -
11A ILE* 4.2 0.6 - - - +
102A LEU 3.4 1.7 - - - +
103A ALA* 3.6 2.1 - - - -
104A LEU* 2.8 50.0 + - + +
108A GLN* 3.8 15.1 + - - +
109A PRO* 5.4 1.6 - - - +
110A GLU* 2.5 29.6 + - - +
111A PRO* 1.3 72.6 + - - +
113A ILE* 1.3 69.4 + - - +
114A ILE* 3.9 25.6 - - + -
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Residues in contact with ILE 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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3A GLU 4.9 1.1 - - - +
4A GLU* 4.4 24.0 - - + +
7A GLY 3.9 10.1 - - - -
8A MET* 3.6 20.0 - - + +
11A ILE* 3.8 13.2 - - + -
101A ASN* 3.3 36.3 - - + +
102A LEU 3.4 2.2 - - - +
103A ALA* 3.8 22.2 - - + -
112A THR* 1.3 84.1 - - - +
114A ILE* 1.3 68.8 + - - +
115A ASN 4.4 0.4 + - - +
152A TYR* 3.4 19.5 - - - +
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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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101A ASN* 3.2 6.9 - - - -
102A LEU* 2.8 43.3 + - + +
104A LEU* 3.8 26.7 - - + -
112A THR* 3.9 20.6 - - + -
113A ILE* 1.3 77.0 - - - +
115A ASN* 1.3 62.1 + - - +
116A VAL* 3.3 12.3 + - + -
140A TYR* 3.4 46.4 - - + +
146A TYR* 4.6 11.7 - - + +
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Residues in contact with ASN 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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99A ASN* 2.8 36.5 + - - +
100A CYS 3.2 10.3 + - - -
101A ASN* 3.1 21.6 + - - +
113A ILE* 4.3 0.8 + - - +
114A ILE* 1.3 72.2 - - - +
116A VAL* 1.3 59.7 + - - +
117A GLY* 3.6 10.5 + - - +
140A TYR* 3.7 18.2 - - - -
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Residues in contact with VAL 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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100A CYS* 3.0 21.3 + - + +
101A ASN 4.5 0.7 - - - -
102A LEU* 3.8 34.8 - - + -
114A ILE* 3.3 12.1 + - + -
115A ASN* 1.3 75.6 - - - +
117A GLY* 1.3 62.9 + - - +
118A ASP 4.6 0.2 - - - +
119A VAL* 4.4 0.7 - - + -
138A TYR* 3.8 33.4 - - + +
139A SER 3.5 21.1 + - - +
140A TYR* 4.1 16.4 - - + -
142A THR* 5.2 0.2 - - + -
151A LEU* 3.8 27.1 - - + -
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Residues in contact with GLY 117 (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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99A ASN* 3.8 13.2 - - - -
100A CYS* 2.8 28.7 + - - -
115A ASN* 3.4 15.8 + - - -
116A VAL* 1.3 79.9 - - - +
118A ASP* 1.3 64.8 + - - -
119A VAL* 3.7 4.5 + - - +
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Residues in contact with ASP 118 (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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97A TYR 4.4 0.2 - - - +
98A PRO* 3.1 15.3 - - + +
99A ASN* 2.6 34.6 + - - +
116A VAL 4.6 0.2 - - - +
117A GLY* 1.3 73.3 - - - -
119A VAL* 1.3 60.6 - - - +
120A VAL* 4.3 6.2 + - + +
137A LYS 3.9 0.7 - - - +
138A TYR* 3.8 17.3 - - - +
139A SER 4.5 2.9 + - - -
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Residues in contact with VAL 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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96A ASP* 3.5 4.0 - - - +
97A TYR* 2.8 49.1 + - + +
100A CYS* 3.7 28.9 - - + -
116A VAL* 4.4 0.7 - - + -
117A GLY 4.0 1.8 - - - +
118A ASP* 1.3 76.8 - - - +
120A VAL* 1.3 64.0 + - - +
136A LEU* 3.7 39.7 - - + -
137A LYS 3.3 6.1 - - - +
138A TYR* 3.7 26.0 - - + -
151A LEU* 4.1 11.7 - - + -
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Residues in contact with VAL 120 (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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96A ASP* 3.5 20.2 - - + +
118A ASP* 4.2 6.5 - - + +
119A VAL* 1.3 79.1 - - - +
121A SER* 1.3 72.1 + - - +
122A TYR* 5.3 2.0 - - + -
136A LEU* 4.4 3.6 - - - -
137A LYS* 2.8 57.4 + - + +
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Residues in contact with SER 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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94A GLU* 3.1 39.5 + - - -
96A ASP* 2.8 12.2 + - - -
120A VAL* 1.3 80.8 - - - +
122A TYR* 1.3 61.5 + - - +
134A ARG* 4.3 15.2 + - - +
135A MET 3.3 9.0 - - - -
136A LEU* 4.2 12.1 - - - +
173A MET* 5.2 0.4 - - - -
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Residues in contact with TYR 122 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 5.3 2.7 - - + -
121A SER* 1.3 77.3 - - - +
123A GLY* 1.3 81.1 + - - +
124A ASN* 3.5 2.0 + - - -
125A ILE* 5.0 10.9 - - + +
134A ARG* 3.4 4.2 - - - -
135A MET* 2.7 36.3 + - + +
137A LYS* 3.9 44.4 - - + -
170A PHE* 4.1 23.8 - + + -
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Residues in contact with GLY 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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122A TYR* 1.3 98.2 - - - +
124A ASN* 1.3 70.5 + - - +
125A ILE* 3.5 2.9 + - - +
132A THR* 6.4 1.1 - - - -
133A ALA 3.5 7.6 - - - -
134A ARG* 4.5 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