Contacts of the strand formed by residues 106 - 112 (chain A) in PDB entry 2WQN
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 GLU 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A LEU* 5.4 0.2 - - - +
64A LYS* 3.6 36.6 + - - +
65A VAL 3.2 15.7 - - - +
66A GLN* 2.7 34.5 + - - +
67A ILE* 4.6 4.0 - - - -
101A PHE 3.5 0.3 - - - +
102A ILE* 3.1 7.8 - - - +
103A GLU 2.8 36.2 + - - +
104A ASP* 3.1 16.8 - - - +
105A ASN* 1.3 85.9 - - - +
107A LEU* 1.3 65.5 + - - +
108A ASN* 3.6 3.3 + - - +
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Residues in contact with LEU 107 (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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63A LYS 3.5 4.0 - - - +
64A LYS* 3.5 1.0 - - - -
65A VAL* 2.9 37.6 + - + +
67A ILE* 3.9 34.6 - - + +
79A CYS* 4.8 16.6 - - - -
80A ILE* 5.0 19.5 - - + -
83A ILE* 4.8 7.2 - - + -
100A SER* 4.2 9.2 - - - -
101A PHE* 3.7 25.1 - - - +
102A ILE* 4.6 2.5 - - + +
106A GLU* 1.3 70.9 - - - +
108A ASN* 1.3 69.3 + - - +
109A ILE* 3.8 25.1 - - + -
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Residues in contact with ASN 108 (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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31A LEU* 3.9 10.4 - - - +
62A LEU* 4.0 8.9 - - + +
63A LYS 3.3 3.6 - - - -
64A LYS* 3.4 36.0 - - - +
100A SER* 3.0 5.7 - - - -
101A PHE* 2.8 73.7 + - + -
103A GLU* 3.3 28.1 + - - +
106A GLU* 3.6 8.5 + - - +
107A LEU* 1.3 73.0 - - - +
109A ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 109 (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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61A ALA 3.6 1.6 - - - +
62A LEU* 3.5 3.7 - - - -
63A LYS* 2.9 55.4 + - + +
65A VAL* 4.9 6.1 - - + -
79A CYS* 6.1 0.2 - - - -
83A ILE* 3.7 25.1 - - + -
97A TYR* 4.1 14.6 - - + -
99A ALA 3.6 9.2 - - - +
100A SER* 4.5 7.0 - - - -
107A LEU* 3.8 27.1 - - + +
108A ASN* 1.3 75.5 - - - +
110A VAL* 1.3 62.6 + - - +
111A LEU* 3.9 29.0 + - + +
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Residues in contact with VAL 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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28A TYR* 3.8 28.5 - - + +
34A PHE* 3.7 22.0 - - + -
60A VAL* 3.7 34.8 - - + -
61A ALA 3.5 2.9 - - - +
62A LEU* 4.5 12.3 - - + +
97A TYR* 3.7 3.3 - - - -
98A TYR* 3.0 26.2 + - + -
99A ALA* 2.9 21.4 + - + +
101A PHE* 4.0 17.0 - - + -
109A ILE* 1.3 75.4 - - - +
111A LEU* 1.3 61.7 + - - +
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Residues in contact with LEU 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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60A VAL* 3.4 8.3 - - - +
61A ALA* 2.8 38.1 + - + +
63A LYS* 4.1 26.5 - - + -
95A ILE* 4.1 8.3 - - + -
96A LYS 3.3 6.3 - - - +
97A TYR* 3.5 46.9 - - + -
98A TYR* 3.7 5.2 - - - -
109A ILE* 3.9 10.5 - - + +
110A VAL* 1.3 76.1 - - - +
112A GLU* 1.3 66.4 + - - +
113A LEU 3.3 0.5 + - - -
179A ASP* 3.7 26.0 - - + +
1301A ADP 3.9 14.4 - - + +
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Residues in contact with GLU 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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59A PRO 5.3 0.2 - - - -
91A HIS 5.4 0.2 - - - +
94A VAL 3.6 9.2 - - - +
95A ILE* 3.7 12.1 - - + +
96A LYS* 2.9 47.0 + - + +
98A TYR* 3.6 21.5 - - - +
111A LEU* 1.3 69.9 - - - +
113A LEU* 1.3 71.1 + - - +
114A ALA 3.4 0.5 + - - -
176A LYS* 2.6 39.2 + - - +
1301A ADP 2.9 24.1 + - - -
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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