Contacts of the strand formed by residues 96 - 102 (chain H) in PDB entry 2QXU
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 VAL 96 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70H LYS* 3.9 14.5 + - - +
71H VAL* 3.4 14.1 - - + +
73H ILE* 4.0 18.4 - - + -
86H TYR* 3.9 23.1 - - + -
87H ILE* 4.5 7.6 - - + -
92H GLY 3.5 16.1 + - - +
93H GLY 5.1 1.4 - - - +
94H ASN 3.7 0.2 - - - -
95H LYS* 1.3 86.2 + - - +
97H ALA* 1.3 65.8 + - - +
98H ASN 4.2 3.1 - - - +
99H VAL* 3.5 32.3 - - + -
121H GLN* 4.9 0.3 + - - +
123H ILE* 3.3 28.1 - - + +
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ASN* 3.4 17.7 - - - +
70H LYS* 4.2 7.2 - - + +
71H VAL 3.0 9.4 + - - +
72H ASP* 3.3 11.7 - - - +
96H VAL* 1.3 74.5 - - - +
98H ASN* 1.3 71.1 + - - +
121H GLN* 3.9 23.3 - - - +
122H LYS 4.5 0.9 - - - +
123H ILE* 3.4 9.5 - - - +
124H LEU* 3.0 24.8 + - - +
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Residues in contact with ASN 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H ASN* 4.9 2.0 - - - +
72H ASP* 2.9 35.0 + - + +
73H ILE 2.8 25.6 + - - +
96H VAL* 4.2 0.3 - - - +
97H ALA* 1.3 86.3 - - - +
99H VAL* 1.3 63.6 + - - +
124H LEU* 3.7 19.1 - - + +
172H GLY 3.5 22.4 - - - +
173H LEU* 3.4 17.9 + - + +
174H ASN 4.5 0.2 - - - -
175H GLY* 3.5 22.0 - - - +
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Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ILE* 3.4 9.9 - - + +
75H ALA* 5.8 0.2 - - + -
83H THR* 4.3 18.8 - - + -
87H ILE* 4.4 7.6 - - + -
96H VAL* 3.5 29.4 - - + -
98H ASN* 1.3 73.1 - - - +
100H VAL* 1.3 69.2 + - - +
101H THR* 4.0 20.0 - - + -
123H ILE* 3.7 14.1 - - + -
124H LEU 2.8 10.6 + - - +
125H TYR* 3.3 32.8 - - + -
126H THR* 3.0 24.6 + - - -
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Residues in contact with VAL 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ILE 2.8 11.1 + - - +
74H VAL* 3.2 9.7 - - + +
75H ALA* 2.8 25.1 + - - +
99H VAL* 1.3 80.4 - - - +
101H THR* 1.3 63.8 + - - +
102H LEU* 4.1 3.6 - - + -
126H THR* 3.3 15.3 - - + +
128H ILE* 3.7 25.1 - - + -
169H ILE* 3.9 24.9 - - + +
172H GLY* 4.0 32.1 - - - -
173H LEU* 4.2 15.5 - - + +
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Residues in contact with THR 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H ALA* 3.2 9.6 - - + -
80H GLY* 4.1 13.5 - - - +
83H THR* 5.7 1.3 - - + -
84H LEU* 6.0 2.2 - - + -
99H VAL* 4.0 17.9 - - + -
100H VAL* 1.3 78.8 - - - +
102H LEU* 1.3 67.6 + - - +
104H GLY* 4.4 7.8 + - - -
106H ASN* 3.2 39.3 + - - +
125H TYR* 5.5 4.0 - - + -
126H THR 3.0 6.9 + - - +
127H SER* 3.3 16.6 + - - -
128H ILE* 2.9 26.5 + - - +
143H LEU* 5.6 2.0 - - + -
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H PHE* 4.7 5.4 - - + -
22H ILE* 5.1 6.1 - - + -
74H VAL* 4.0 21.8 - - + -
75H ALA 2.6 15.8 + - - +
76H HIS* 3.2 14.4 - - + -
77H SER 2.9 21.0 + - - -
100H VAL* 4.1 3.6 - - + -
101H THR* 1.3 80.0 - - - +
103H GLY* 1.3 66.7 + - - +
128H ILE* 3.5 12.8 - - + -
159H LEU* 3.7 28.0 - - + +
160H LEU* 4.3 17.0 - - + -
165H VAL* 3.9 7.2 - - + -
169H ILE* 3.3 35.7 - - + -
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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