Contacts of the strand formed by residues 109 - 115 (chain A) in PDB entry 2I6A
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 ASP 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A ASN* 3.0 31.1 + - - +
82A LYS* 3.5 39.0 + - + +
84A ALA 3.1 13.5 + - - +
85A THR* 3.6 2.4 - - - +
86A PHE 3.5 15.4 + - - -
107A HIS 3.8 1.8 + - - -
108A VAL* 1.3 68.4 - - - +
110A ALA* 1.3 59.9 + - - +
111A HIS* 2.8 39.1 + - - -
158A LEU* 4.0 3.6 - - - +
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Residues in contact with ALA 110 (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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86A PHE* 3.5 15.0 - - + +
103A ALA* 4.0 15.7 - - + -
108A VAL* 3.1 8.1 + - + +
109A ASP* 1.3 75.5 - - - +
111A HIS* 1.3 75.5 + - - +
112A TYR* 3.5 35.6 - - + +
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Residues in contact with HIS 111 (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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86A PHE 2.9 15.5 + - - +
87A PHE* 3.2 37.5 - + + -
88A GLY 3.5 0.9 + - - -
109A ASP* 2.8 45.3 + - - -
110A ALA* 1.3 76.2 + - - +
112A TYR* 1.3 62.7 + - - +
149A HIS* 3.9 10.9 + - + +
155A ASN* 4.6 11.0 + - - +
158A LEU* 3.1 33.3 - - + +
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Residues in contact with TYR 112 (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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15A PRO* 3.8 28.7 - - + -
67A GLN* 2.6 24.7 + - - -
86A PHE* 3.9 11.5 - + - -
88A GLY 3.1 17.5 - - - +
90A ILE* 3.5 27.4 - - + -
99A LEU* 3.8 6.1 + - + +
100A LYS* 3.8 39.7 - - + -
103A ALA* 3.4 15.9 - - - +
110A ALA* 3.5 23.6 - - + +
111A HIS* 1.3 79.1 - - - +
113A TYR* 1.3 60.3 + - - +
114A GLU* 3.8 12.4 + - + +
149A HIS* 3.8 10.6 + - - -
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Residues in contact with TYR 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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88A GLY 2.8 13.0 + - - +
89A CYS* 3.3 25.7 - - + -
90A ILE 3.0 24.2 + - - +
112A TYR* 1.3 70.3 - - - +
114A GLU* 1.3 59.6 + - - +
115A GLN* 3.7 26.1 - - + +
143A CYS* 5.0 7.9 - - + -
144A TYR* 4.5 6.5 - + + -
145A LYS 6.1 0.4 - - - -
148A LYS* 3.4 62.8 + - + +
149A HIS* 3.7 24.1 - + + -
116C ASN* 3.5 30.9 + - + +
117C GLU* 4.8 9.0 + - - -
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Residues in contact with GLU 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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90A ILE* 3.4 22.2 - - + +
91A GLY 4.4 5.0 - - - +
92A ILE* 3.8 21.8 - - + +
100A LYS* 3.1 42.7 + - - +
112A TYR* 3.8 13.3 + - + +
113A TYR* 1.3 77.2 - - - +
115A GLN* 1.3 63.0 - - - +
92C ILE* 4.1 32.0 - - + +
116C ASN* 3.1 27.6 + - - +
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Residues in contact with GLN 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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89A CYS* 3.9 10.3 - - - -
90A ILE 2.7 25.1 + - - +
91A GLY* 3.2 1.7 - - - -
92A ILE* 3.0 29.1 + - - +
113A TYR* 3.7 27.1 - - + +
114A GLU* 1.3 75.7 - - - +
116A ASN* 1.3 59.5 + - - +
117A GLU* 3.2 23.4 + - - +
118A GLN* 2.6 50.9 - - - +
140A ALA* 3.6 2.8 - - - +
143A CYS* 3.9 15.0 - - + -
116C ASN* 5.5 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