Contacts of the strand formed by residues 81 - 86 (chain K) in PDB entry 2WW9
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 ILE 81 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K ALA 4.2 0.3 - - - +
75K LYS* 3.4 38.7 + - + +
76K VAL* 3.2 28.6 + - - +
78K ASP* 5.0 5.2 - - + -
79K GLY* 3.8 17.3 - - - +
80K ASN* 1.4 77.7 - - - +
82K LEU* 1.4 73.6 + - - +
83K VAL* 5.2 0.2 - - + -
123K TYR* 3.6 42.8 - - + +
124K VAL 3.4 8.7 - - - +
125K ARG* 3.8 22.7 - - + -
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Residues in contact with LEU 82 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73K MET* 5.8 3.4 - - + -
76K VAL* 4.1 23.1 - - + -
81K ILE* 1.4 78.7 - - - +
83K VAL* 1.3 64.0 + - - +
84K PHE* 3.7 34.8 - - + -
103K TYR* 4.0 17.0 - - + -
124K VAL* 2.9 30.5 + - - +
126K LEU* 3.6 16.4 - - + +
130K TYR* 3.4 26.0 - - + +
132K ALA* 5.2 3.6 - - + +
135K ILE* 5.4 2.7 - - + +
136K ALA* 4.6 12.6 - - + -
139K ILE* 4.3 18.2 - - + -
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Residues in contact with VAL 83 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66K PRO* 3.9 5.2 - - - +
67K ILE* 3.3 39.3 + - + +
72K ALA* 3.4 42.8 - - + +
75K LYS* 4.6 17.3 - - + +
82K LEU* 1.3 77.9 - - - +
84K PHE* 1.3 70.7 + - - +
121K LYS* 4.7 10.5 - - + -
122K ALA 3.3 21.1 - - - +
123K TYR* 4.2 9.6 - - + -
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Residues in contact with PHE 84 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K ILE* 3.8 29.2 - - + -
65K GLN 3.8 2.9 - - - +
66K PRO* 3.7 25.1 - - + -
67K ILE* 3.7 8.4 - - - +
82K LEU* 3.7 31.4 - - + -
83K VAL* 1.3 76.0 - - - +
85K GLN* 1.3 63.7 + - - +
86K VAL* 4.1 17.5 - - + -
95K ILE* 5.5 1.1 - - + -
99K VAL* 3.9 21.8 - - + -
103K TYR* 3.6 37.0 - + - -
121K LYS* 3.4 5.2 - - - -
122K ALA* 2.9 30.2 + - + +
124K VAL* 4.0 22.2 - - + -
139K ILE* 5.4 0.2 - - + -
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Residues in contact with GLN 85 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63K ILE* 4.0 0.7 - - - -
64K GLU* 3.1 16.8 + - - +
65K GLN* 2.9 56.3 + - + +
67K ILE* 3.7 21.7 - - + +
84K PHE* 1.3 77.0 - - - +
86K VAL* 1.3 61.3 + - - +
115K ARG* 3.2 46.6 + - - +
117K ASN* 3.7 7.5 + - - +
119K THR* 3.5 31.2 - - - +
120K LYS 3.5 6.3 - - - +
121K LYS* 4.8 4.4 + - - +
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Residues in contact with VAL 86 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62K VAL 3.4 9.9 - - - +
63K ILE* 4.0 21.5 - - + +
64K GLU* 4.5 1.6 - - - -
84K PHE* 4.1 9.9 - - + -
85K GLN* 1.3 78.8 - - - +
87K SER* 1.4 66.2 + - - +
90K ALA* 3.5 24.2 - - + -
95K ILE* 4.0 23.3 - - + -
119K THR* 2.9 15.9 + - - -
120K LYS* 2.9 37.2 + - + +
122K ALA* 4.0 19.7 - - + -
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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