Contacts of the strand formed by residues 67 - 74 (chain L) in PDB entry 2WWB
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 67 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55L GLU* 5.5 0.7 - - - +
56L VAL 3.5 7.0 - - - +
57L LEU* 3.8 18.2 - - + -
66L GLN* 1.4 82.5 + - - +
68L GLY* 1.4 59.3 + - - +
82L VAL* 4.4 5.4 - - - +
83L ASP 4.3 4.9 - - - +
107L THR* 3.1 30.7 + - - +
108L LYS* 3.2 27.0 + - - +
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Residues in contact with GLY 68 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55L GLU* 4.4 8.0 + - - +
56L VAL* 3.1 31.6 + - - +
67L GLU* 1.4 78.9 - - - +
69L LYS* 1.4 65.1 + - - +
70L ILE* 3.8 0.7 + - - +
82L VAL* 3.7 8.3 - - - +
83L ASP 3.7 15.3 - - - -
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Residues in contact with LYS 69 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ARG* 4.8 9.6 - - - +
53L ASP* 3.1 48.2 + - - +
54L ASP 4.0 7.6 - - - +
55L GLU* 3.6 29.0 + - + +
68L GLY* 1.4 71.7 - - - -
70L ILE* 1.3 63.9 + - - +
71L SER 3.7 0.2 - - - -
82L VAL* 3.7 0.9 - - - +
83L ASP* 3.0 39.7 + - + +
110L HIS* 5.1 2.4 - - - -
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Residues in contact with ILE 70 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50L ILE* 3.5 32.8 - - + -
51L ARG 4.3 4.9 - - - +
52L ARG* 2.8 38.3 + - - +
54L ASP 3.6 9.8 + - - +
56L VAL* 3.5 38.8 - - + -
69L LYS* 1.3 70.9 - - - +
71L SER* 1.4 59.2 + - - +
72L SER 3.3 29.2 - - - +
73L VAL* 4.3 11.7 - - + -
80L VAL* 3.6 24.2 - - + -
81L GLN 3.6 5.6 - - - +
82L VAL* 4.3 4.9 - - + -
104L LEU* 5.0 0.2 - - + -
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Residues in contact with SER 71 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ARG* 2.9 27.2 + - - +
69L LYS 3.4 4.0 + - - -
70L ILE* 1.4 70.7 - - - +
72L SER* 1.4 60.3 + - - +
81L GLN* 3.0 46.8 + - - +
83L ASP* 3.7 29.4 + - - -
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Residues in contact with SER 72 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D A 5.0 0.2 - - - -
52L ARG* 4.4 7.6 - - - +
70L ILE* 3.3 11.0 - - - +
71L SER* 1.4 82.3 + - - +
73L VAL* 1.4 63.8 + - - +
74L TYR* 3.4 39.6 + - - -
81L GLN* 2.9 32.2 + - - +
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Residues in contact with VAL 73 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D A 3.3 59.4 + - - +
73D U 4.0 6.6 + - - -
31L LEU* 3.4 38.8 - - + +
50L ILE* 4.4 5.2 - - + -
70L ILE* 4.3 8.1 - - + -
72L SER* 1.4 80.3 + - - +
74L TYR* 1.4 65.5 + - - +
79L ALA 3.3 15.7 - - - +
80L VAL* 3.5 20.9 - - + -
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Residues in contact with TYR 74 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D U 4.2 5.2 - - - -
76D C 6.2 0.2 - - - -
31L LEU* 4.5 1.7 - - - +
72L SER* 3.4 35.9 + - - -
73L VAL* 1.4 77.2 - - - +
75L ARG* 1.4 59.3 + - - +
76L LEU* 4.7 1.1 - - + +
77L LYS* 3.9 28.0 - - + +
78L PHE* 3.1 26.5 + - - -
79L ALA 3.0 19.7 + - - +
81L GLN* 4.2 15.3 + - + -
98L ASN* 3.7 28.7 - - - -
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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