Contacts of the strand formed by residues 110 - 116 (chain A) in PDB entry 2A4X
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 GLN 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A ASN 3.7 0.3 - - - -
106A ALA* 2.9 29.9 + - - +
108A TRP* 3.0 31.3 + - + +
109A GLY* 1.3 83.8 - - - +
111A ARG* 1.3 69.0 + - - +
112A TYR* 3.3 10.9 + - + -
126A PHE* 3.5 20.9 - - + -
127A ALA 3.2 13.7 - - - +
128A PRO* 4.4 7.6 - - + +
129A LEU* 3.6 8.2 - - - +
700A BLM 3.0 55.7 + - + +
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Residues in contact with ARG 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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82A THR* 3.5 39.5 - - + +
85A VAL* 4.1 9.4 - - + -
86A ASP* 2.7 43.0 + - - +
103A PRO* 3.6 22.5 + - + +
104A TRP* 3.5 16.9 - - - +
105A ASN* 3.0 37.5 + - - +
110A GLN* 1.3 71.6 - - - +
112A TYR* 1.3 58.7 + - - +
126A PHE* 3.1 9.1 - - - +
127A ALA* 2.8 35.8 + - + +
129A LEU* 3.7 7.1 - - + +
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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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76A ALA* 4.7 4.2 - - - +
85A VAL* 4.9 1.3 - - - -
103A PRO* 3.1 4.4 - - - +
104A TRP* 2.8 69.5 + + + +
106A ALA* 4.0 14.1 - - + -
108A TRP* 3.7 22.4 - + - -
110A GLN* 3.7 11.9 - - + -
111A ARG* 1.3 74.5 - - - +
113A ALA* 1.3 67.1 + - - +
114A ILE* 4.2 6.1 - - + -
124A ASP* 3.1 44.7 + - + +
125A LEU 3.4 2.9 - - - -
126A PHE* 3.4 31.2 - + + -
700A BLM 3.5 29.6 + - - -
207B LEU* 5.9 1.7 - - - +
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Residues in contact with ALA 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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85A VAL* 4.4 4.9 - - + -
89A TYR* 3.8 20.0 - - + -
101A LEU 3.5 12.3 - - - +
103A PRO* 3.9 16.2 - - + -
104A TRP* 4.1 2.9 - - - -
112A TYR* 1.3 80.5 - - - +
114A ILE* 1.3 70.3 + - - +
124A ASP* 3.5 1.9 - - - -
125A LEU* 2.9 43.5 + - + +
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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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89A TYR* 3.5 5.9 - - - -
100A HIS* 2.8 37.5 + - + -
101A LEU* 2.9 50.9 + - + +
104A TRP* 4.3 7.9 - - + -
112A TYR* 4.2 8.5 - - + -
113A ALA* 1.3 83.1 - - - +
115A VAL* 1.3 69.2 + - - +
116A LYS* 4.7 0.7 - - - +
122A VAL* 3.6 27.6 - - + -
123A VAL 3.5 6.1 - - - +
124A ASP* 3.6 14.4 - - - +
125A LEU* 5.4 0.2 - - - -
700A BLM 3.8 27.4 - - + -
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Residues in contact with VAL 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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21A PHE* 4.0 9.6 - - + -
89A TYR* 3.6 27.6 - - + +
92A LEU* 4.0 33.2 - - + -
93A VAL* 5.2 0.9 - - + -
97A TYR* 5.6 1.1 - - + -
98A GLU 3.1 15.5 - - - +
99A GLY* 4.2 2.2 - - - -
100A HIS* 4.0 1.1 - - - +
114A ILE* 1.3 85.1 - - - +
116A LYS* 1.3 68.5 + - - +
122A VAL* 3.9 0.9 - - - -
123A VAL* 3.0 48.2 + - + +
125A LEU* 4.3 12.6 - - + -
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Residues in contact with LYS 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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21A PHE* 3.6 15.1 - - - -
71A HIS* 5.3 1.4 + - - -
97A TYR* 4.3 3.3 - - - +
98A GLU* 3.0 52.7 + - + +
100A HIS* 3.7 41.9 + - + +
114A ILE* 4.7 0.6 - - - +
115A VAL* 1.3 80.8 - - - +
117A ASP* 1.3 68.1 + - - +
120A GLY* 3.6 26.0 - - - +
121A ASN 3.1 10.5 - - - +
122A VAL* 3.1 29.7 - - - +
700A BLM 6.1 0.4 - - - +
261B ASP* 5.7 2.0 + - - -
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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