Contacts of the strand formed by residues 119 - 125 (chain A) in PDB entry 2QQK
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 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A ILE* 4.4 12.1 - - + -
59A VAL 3.3 7.6 - - - +
60A TYR* 4.2 15.0 - - + -
68A ILE* 4.7 0.9 - - - -
93A GLY* 2.9 38.4 + - - +
94A ASP* 3.8 28.3 - - + +
115A SER* 3.4 12.2 + - - -
117A GLY 3.5 1.0 - - - -
118A SER* 1.3 91.4 + - - +
120A LEU* 1.3 63.0 + - - +
221A HIS* 5.9 7.6 - - + +
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Residues in contact with LEU 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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58A ILE* 3.4 7.3 - - - +
59A VAL* 2.9 38.9 + - + +
68A ILE* 3.9 22.7 - - + +
70A LEU* 3.4 45.8 - - + -
90A ILE* 4.1 5.8 - - + -
91A ARG 3.4 11.0 - - - +
92A ASP* 4.2 2.5 - - - -
93A GLY 3.4 6.8 - - - +
101A LEU* 3.4 33.2 - - + -
113A ILE* 4.7 5.6 - - + +
115A SER* 4.2 14.6 - - - -
119A MET* 1.3 77.7 - - - +
121A TYR* 1.3 60.4 + - - +
122A ILE* 5.0 2.5 - - + -
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Residues in contact with TYR 121 (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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56A GLU* 2.8 39.2 + - + +
57A TRP 3.6 3.6 - - - -
58A ILE* 3.8 24.0 - - + -
89A GLU* 5.4 0.4 - - + -
90A ILE* 3.5 3.8 - - - +
91A ARG* 2.8 64.5 + - + +
93A GLY 3.6 0.6 + - - -
94A ASP* 4.0 7.4 - - - -
95A SER* 3.8 30.5 - - - +
96A GLU* 3.9 29.3 + - + +
120A LEU* 1.3 73.6 - - - +
122A ILE* 1.3 63.4 + - - +
123A LYS* 3.8 37.8 - - + +
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Residues in contact with ILE 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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40A ILE* 4.1 21.5 - - + -
56A GLU* 3.1 6.2 - - - +
57A TRP* 2.8 57.9 + - + +
59A VAL* 4.4 10.3 - - + -
70A LEU* 3.5 31.6 - - + -
88A ILE* 3.7 29.6 - - + -
89A GLU 3.5 6.1 - - - +
90A ILE* 4.3 7.2 - - + -
120A LEU* 5.0 2.9 - - + -
121A TYR* 1.3 82.2 - - - +
123A LYS* 1.3 62.2 + - - +
135A PHE* 5.1 1.1 - - + -
137A LEU* 3.8 15.9 - - + -
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Residues in contact with LYS 123 (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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54A ASN* 4.6 16.7 - - + +
55A CYS 3.3 15.7 - - - +
56A GLU* 4.7 2.0 - - + -
87A PHE* 4.0 3.9 - - - +
88A ILE* 3.7 1.8 - - - -
89A GLU* 2.9 62.2 + - + +
96A GLU* 2.9 27.6 + - - +
121A TYR* 3.8 24.8 - - + +
122A ILE* 1.3 77.2 - - - +
124A PHE* 1.3 59.5 + - - +
125A THR* 3.4 25.9 + - - +
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Residues in contact with PHE 124 (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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42A SER* 4.0 18.8 - - - -
43A PRO* 4.5 10.1 - - + -
49A TYR* 3.6 53.2 - + + -
50A PRO* 5.3 0.4 - - + -
53A GLN* 4.9 9.0 - - - -
54A ASN* 3.3 5.5 - - - +
55A CYS* 2.8 35.3 + - + +
57A TRP* 4.0 16.9 - - + -
78A ILE* 3.7 26.7 - - + -
87A PHE 3.4 15.5 - - - -
88A ILE* 4.4 2.7 - - + +
123A LYS* 1.3 72.7 - - - +
125A THR* 1.3 71.7 + - - +
126A SER* 4.4 5.4 - - - -
135A PHE* 3.6 29.4 - + + -
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Residues in contact with THR 125 (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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54A ASN* 3.4 21.3 - - - +
85A TYR 4.0 14.6 - - - +
86A ASP* 3.5 3.3 - - - +
87A PHE* 3.0 62.9 + - + +
123A LYS* 3.4 27.4 + - - +
124A PHE* 1.3 81.0 - - - +
126A SER* 1.3 68.0 + - - +
127A ASP* 5.7 0.9 - - + -
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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