Contacts of the strand formed by residues 94 - 100 (chain A) in PDB entry 4QNA
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 LYS 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ILE* 3.9 24.9 - - + -
55A ILE 3.3 7.4 - - - +
56A ASP* 3.1 34.5 + - + +
57A LEU* 4.4 4.4 - - - +
90A LEU* 3.9 3.3 - - - +
91A LYS* 2.9 49.4 + - - +
92A ASP* 4.2 2.0 - - + +
93A THR* 1.3 99.9 - - - +
95A LEU* 1.3 61.6 + - - +
96A TRP* 4.3 8.5 - - + +
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Residues in contact with LEU 95 (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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16A LEU* 4.1 21.5 - - + -
53A LYS 3.4 3.6 - - - +
54A ILE* 3.5 1.7 - - - -
55A ILE* 2.7 41.4 + - + +
57A LEU* 3.8 24.4 - - + +
67A ILE* 3.6 22.4 - - + -
71A ILE* 3.5 25.1 - - + -
88A SER* 4.2 5.4 - - - -
89A TYR 3.4 27.4 - - - +
90A LEU* 4.6 7.0 - - + +
94A LYS* 1.3 74.3 - - - +
96A TRP* 1.3 62.7 + - - +
97A ILE* 3.9 12.7 + - + -
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Residues in contact with TRP 96 (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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20A PRO* 3.4 28.7 - - + -
21A GLU* 3.9 24.0 - - + -
24A PHE* 4.8 7.4 - - + -
26A LYS* 3.8 35.2 - - + -
52A ILE* 3.7 33.2 - - + -
53A LYS 3.6 3.4 - - - -
54A ILE* 3.2 30.0 - - + +
87A GLY 3.8 1.2 - - - +
88A SER* 3.2 4.9 - - - -
89A TYR* 2.7 49.1 + - + +
91A LYS* 3.8 40.3 - - + +
94A LYS* 4.3 9.1 - - + +
95A LEU* 1.3 75.5 - - - +
97A ILE* 1.3 62.7 + - - +
98A ILE* 3.8 8.0 + - + -
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Residues in contact with ILE 97 (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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51A ALA 3.6 2.4 - - - +
52A ILE* 3.6 0.2 - - - -
53A LYS* 2.8 65.5 + - + +
55A ILE* 4.4 4.9 - - + -
67A ILE* 4.4 10.1 - - + -
70A GLU* 4.4 12.3 - - - +
71A ILE* 3.8 19.3 - - + -
74A LEU* 3.9 26.0 - - + -
85A TYR* 4.1 13.7 - - + -
87A GLY 3.9 2.2 - - - -
88A SER* 4.1 7.4 - - - +
95A LEU* 4.1 20.2 - - + +
96A TRP* 1.3 74.6 - - - +
98A ILE* 1.3 61.3 + - - +
99A MET* 3.9 11.9 - - + +
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Residues in contact with ILE 98 (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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20A PRO* 4.6 0.2 - - + -
24A PHE* 3.4 42.6 - - + -
50A VAL* 3.8 28.9 - - + -
51A ALA 3.5 3.8 - - - +
52A ILE* 4.2 14.6 - - + -
85A TYR* 4.0 1.4 - - - -
86A TYR* 2.8 40.8 + - + +
87A GLY 3.0 18.1 + - - +
89A TYR* 3.8 16.8 - - + -
96A TRP* 4.2 20.9 - - + +
97A ILE* 1.3 74.3 - - - +
99A MET* 1.3 69.1 + - - +
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Residues in contact with MET 99 (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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38A VAL* 5.5 1.3 - - + -
50A VAL* 3.3 9.4 - - - +
51A ALA* 2.8 38.5 + - + +
53A LYS* 4.2 18.4 - - + +
70A GLU* 4.6 6.3 - - - +
74A LEU* 3.8 36.8 - - + -
83A THR* 4.7 1.3 - - - -
84A LYS 3.2 12.8 - - - +
85A TYR* 4.4 4.3 - - + -
86A TYR* 3.6 7.9 - - - -
97A ILE* 3.9 24.0 - - + +
98A ILE* 1.3 80.3 - - - +
100A GLU* 1.3 62.3 + - - +
401A X11 3.3 43.3 - - + +
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Residues in contact with GLU 100 (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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51A ALA* 3.7 1.4 - - - +
82A VAL 3.9 0.7 - - - +
83A THR* 3.5 5.9 - - - -
84A LYS* 2.8 50.0 + - + +
86A TYR* 3.9 10.6 - - + -
99A MET* 1.3 72.7 - - - +
101A TYR* 1.3 70.7 + - - +
102A LEU* 3.9 13.9 + - + +
159A LYS* 2.3 50.7 + - - +
401A X11 2.9 28.2 + - - -
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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