Contacts of the strand formed by residues 96 - 102 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A LYS* 3.8 12.1 + - - +
71A VAL* 3.3 11.7 - - + +
73A ILE* 4.0 27.6 - - + -
86A TYR* 4.0 15.9 - - + -
87A ILE* 4.4 7.4 - - + -
92A GLY 3.5 16.0 + - - +
93A GLY 5.0 0.7 - - - +
94A ASN 3.6 1.5 - - - -
95A LYS* 1.3 87.4 + - - +
97A ALA* 1.3 62.6 + - - +
98A ASN 4.2 5.2 - - - +
99A VAL* 3.4 32.3 - - + -
123A ILE* 3.3 28.9 - - + +
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Residues in contact with ALA 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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4A ASN* 3.5 17.5 - - - +
70A LYS* 4.1 7.2 - - + -
71A VAL 3.0 7.4 + - - +
72A ASP* 3.4 11.7 - - - +
96A VAL* 1.3 76.2 - - - +
98A ASN* 1.3 71.5 + - - +
121A GLN* 3.6 27.9 + - - +
122A LYS 4.4 1.6 - - - +
123A ILE* 3.5 7.5 - - - +
124A LEU* 3.0 25.6 + - - +
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Residues in contact with ASN 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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4A ASN* 4.9 2.2 - - - +
72A ASP* 3.0 34.0 + - + +
73A ILE 2.8 25.8 + - - +
96A VAL* 4.2 0.5 - - - +
97A ALA* 1.3 87.7 - - - +
99A VAL* 1.3 63.3 + - - +
124A LEU* 3.6 18.6 - - - +
172A GLY 3.5 21.1 - - - +
173A LEU* 3.4 19.4 + - + +
175A GLY* 3.6 20.3 - - - +
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Residues in contact with VAL 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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73A ILE* 3.4 11.9 - - + +
83A THR* 4.3 15.5 - - + -
84A LEU* 6.0 0.2 - - + -
87A ILE* 4.3 7.4 - - + -
96A VAL* 3.4 29.8 - - + -
98A ASN* 1.3 73.1 - - - +
100A VAL* 1.3 67.9 + - - +
101A THR* 4.0 20.4 - - + -
123A ILE* 3.6 15.7 - - + -
124A LEU 2.8 9.9 + - - +
125A TYR* 3.3 32.0 - - + -
126A THR* 2.9 24.9 + - - +
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Residues in contact with VAL 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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73A ILE 2.8 12.9 + - - +
74A VAL* 3.2 11.7 - - + +
75A ALA 2.8 24.9 + - - -
99A VAL* 1.3 79.8 - - - +
101A THR* 1.3 62.7 + - - +
102A LEU* 3.9 11.4 - - + -
126A THR* 3.3 14.8 - - - +
128A ILE* 3.8 26.0 - - + -
169A ILE* 4.0 18.8 - - + +
172A GLY* 3.9 34.3 - - - -
173A LEU* 4.2 9.4 - - + +
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Residues in contact with THR 101 (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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75A ALA* 3.2 9.2 - - + -
80A GLY* 4.2 14.1 - - - +
83A THR* 5.8 0.9 - - - -
84A LEU* 5.9 2.5 - - + -
99A VAL* 4.0 19.7 - - + -
100A VAL* 1.3 76.8 - - - +
102A LEU* 1.3 65.5 + - - +
103A GLY 4.0 0.4 - - - -
104A GLY* 4.4 6.0 + - - -
106A ASN* 3.2 39.8 + - - +
125A TYR* 5.5 0.7 - - + -
126A THR 3.0 5.0 + - - +
127A SER* 3.4 17.0 + - - -
128A ILE* 2.9 28.1 + - - +
143A LEU* 5.3 5.7 - - + +
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Residues in contact with LEU 102 (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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19A PHE* 4.8 2.0 - - + -
22A ILE* 3.7 29.8 - - + -
74A VAL* 4.0 11.4 - - + -
75A ALA 2.7 16.3 + - - +
76A HIS* 3.2 14.8 - - + -
77A SER 2.9 19.1 + - - -
100A VAL* 3.9 11.0 - - + -
101A THR* 1.3 79.4 - - - +
103A GLY* 1.3 66.9 + - - +
128A ILE* 3.5 29.4 - - + -
159A LEU* 3.9 24.2 - - + +
160A LEU* 4.4 11.4 - - + -
165A VAL* 3.9 11.0 - - + -
169A ILE* 4.0 8.1 - - + -
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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