Contacts of the strand formed by residues 109 - 114 (chain A) in PDB entry 2JQY
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 MET 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A ARG 3.0 15.6 - - - +
93A ASN* 3.3 14.4 - - - +
94A TYR* 3.0 25.7 + - + +
97A HIS* 3.5 46.9 - - + +
107A ALA 4.0 0.2 + - - -
108A ASN* 1.3 72.3 - - - +
110A GLN* 1.3 69.1 + - - +
111A ARG* 3.6 29.1 - - - +
137A PHE* 4.0 14.8 - - + -
138A ALA 3.4 26.9 - - - +
139A ASN* 3.5 10.5 - - + +
142A ASN* 3.8 21.5 - - - +
145A GLY* 6.2 0.2 - - - -
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Residues in contact with GLN 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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91A PHE* 3.1 30.6 - - + -
92A ARG 3.7 0.7 - - - -
93A ASN* 3.2 22.1 + - - +
108A ASN* 4.8 12.4 + - - +
109A MET* 1.3 74.1 - - - +
111A ARG* 1.3 63.6 + - - +
112A TRP* 5.4 2.5 - - + -
138A ALA* 2.6 63.2 + - + +
139A ASN* 5.4 1.8 - - - -
140A ASP* 5.7 4.3 - - - +
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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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90A GLY 3.6 3.6 - - - +
91A PHE* 3.6 5.3 - - - -
92A ARG* 3.0 60.3 + - + +
94A TYR* 4.6 25.4 - - - +
97A HIS* 4.7 14.1 + - - -
109A MET* 3.6 24.4 - - - +
110A GLN* 1.3 82.0 - - - +
112A TRP* 1.3 66.8 + - - +
135A TYR* 5.2 9.6 - - + -
136A LYS 3.2 7.6 - - - +
137A PHE* 3.3 44.5 - - + -
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Residues in contact with TRP 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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89A GLY* 6.5 0.7 - - - -
90A GLY 3.7 3.8 - - - -
91A PHE* 3.0 47.6 - + - -
110A GLN* 5.5 0.9 - - + -
111A ARG* 1.3 75.7 - - - +
113A LYS* 1.3 61.8 + - - +
114A ILE* 4.2 15.9 - - + -
134A MET 3.1 12.8 - - - +
135A TYR* 3.4 6.9 - - - -
136A LYS* 3.1 57.5 + - + -
137A PHE 5.2 0.4 - - - -
138A ALA* 3.6 26.2 - - + -
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Residues in contact with LYS 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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72A GLU* 5.2 11.9 + - + +
88A THR* 2.8 8.4 - - + +
89A GLY* 3.1 0.7 - - - -
90A GLY* 2.7 45.7 + - - +
92A ARG* 3.5 30.7 - - + +
112A TRP* 1.3 76.9 - - - +
114A ILE* 1.3 65.4 + - - +
115A ALA* 6.1 1.1 - - + -
131A TRP* 5.5 14.0 - - - -
133A SER* 4.8 8.1 - - - +
134A MET 3.3 4.7 - - - +
135A TYR* 3.2 37.3 + - + +
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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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87A LEU* 3.4 41.7 - - + -
88A THR 3.2 3.8 - - - +
89A GLY* 4.6 7.0 - - - -
112A TRP* 4.2 16.6 - - + -
113A LYS* 1.3 87.5 - - - +
115A ALA* 1.3 61.8 + - - +
116A PRO* 4.0 6.7 - - + -
132A LEU 2.7 23.0 - - - +
133A SER* 3.8 1.4 - - - -
134A MET* 3.1 39.6 + - + +
136A LYS* 4.9 11.4 - - - -
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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