Contacts of the helix formed by residues 69 - 80 (chain K) 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 SER 69 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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405A ARG* 3.7 17.7 - - - +
1678F G 3.9 25.9 + - - -
67K ILE* 4.0 14.1 - - - +
68K THR* 1.3 76.1 + - - +
70K GLU* 1.4 76.3 + - - +
71K THR* 3.6 6.6 - - - +
72K ALA* 3.4 21.1 + - - +
73K MET* 3.1 25.7 + - - +
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Residues in contact with GLU 70 (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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405A ARG* 3.3 43.6 - - + +
406A GLU 4.2 12.1 - - - +
407A THR 5.1 0.4 - - - +
408A SER* 3.4 41.0 + - - +
1678F G 3.0 43.3 + - - +
69K SER* 1.4 72.9 + - - +
71K THR* 1.4 83.8 + - - +
73K MET* 4.0 1.7 - - - +
74K LYS* 3.2 26.7 + - - +
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Residues in contact with THR 71 (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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1678F G 3.9 9.9 - - - +
67K ILE* 6.1 1.3 - - + -
69K SER* 3.6 7.9 - - - +
70K GLU* 1.4 99.7 + - - +
72K ALA* 1.4 62.6 + - + +
74K LYS* 3.4 7.1 + - - +
75K LYS* 3.0 57.2 + - - +
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Residues in contact with ALA 72 (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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67K ILE* 3.4 19.7 - - + +
68K THR* 4.0 1.6 - - - -
69K SER* 3.4 24.8 + - - +
70K GLU 3.4 0.2 - - - -
71K THR* 1.4 82.6 - - + +
73K MET* 1.4 61.6 + - + +
75K LYS* 3.5 15.3 + - - +
76K VAL* 3.5 16.3 - - - +
81K ILE 4.2 0.3 - - - +
83K VAL* 3.4 33.5 - - + +
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Residues in contact with MET 73 (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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405A ARG* 5.7 3.4 - - - +
408A SER* 5.5 3.8 - - - +
412A GLU* 5.9 5.8 - - + +
67K ILE 5.2 1.3 - - - +
68K THR* 3.4 31.4 - - - +
69K SER 3.1 22.1 + - - +
70K GLU* 4.0 4.5 - - - +
72K ALA* 1.4 75.7 - - + +
74K LYS* 1.4 66.1 + - - +
76K VAL* 3.3 33.4 + - + +
77K GLU* 3.5 16.8 - - - +
82K LEU* 5.9 2.7 - - + -
136K ALA* 5.5 10.8 - - + +
139K ILE* 6.5 1.6 - - + -
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Residues in contact with LYS 74 (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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408A SER* 4.5 9.4 - - - +
70K GLU 3.2 20.1 + - - +
71K THR* 3.8 8.3 - - - +
72K ALA 3.4 0.2 - - - -
73K MET* 1.4 74.4 - - + +
75K LYS* 1.4 59.2 + - - +
77K GLU* 3.1 35.7 + - - +
78K ASP* 2.9 56.8 + - - +
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Residues in contact with LYS 75 (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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71K THR* 3.0 52.8 + - - +
72K ALA* 3.6 11.6 - - - +
73K MET 3.3 0.2 - - - -
74K LYS* 1.4 72.9 - - - +
76K VAL* 1.4 62.3 + - - +
78K ASP* 3.9 9.0 - - - +
79K GLY 3.4 15.6 + - - -
81K ILE* 3.3 41.8 + - + +
83K VAL* 4.8 14.9 - - + +
123K TYR* 3.5 46.0 - - + +
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Residues in contact with VAL 76 (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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72K ALA 3.5 14.8 - - - +
73K MET* 3.3 25.8 - - + +
74K LYS 3.3 0.2 - - - -
75K LYS* 1.4 74.8 - - - +
77K GLU* 1.4 63.0 + - + +
80K ASN* 3.4 22.9 + - - +
81K ILE 3.2 19.4 + - - +
82K LEU* 4.1 16.2 - - + -
132K ALA* 3.2 37.3 - - + +
133K LEU* 4.9 2.7 - - - -
136K ALA* 4.0 9.0 - - + -
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Residues in contact with GLU 77 (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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411A HIS* 5.4 10.4 + - - -
415A ARG* 5.6 5.6 + - - -
73K MET* 3.5 19.3 - - - +
74K LYS* 3.1 40.1 + - - +
76K VAL* 1.4 77.9 - - + +
78K ASP* 1.4 63.0 + - - +
79K GLY 3.6 0.2 + - - -
80K ASN* 4.9 1.2 + - - +
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Residues in contact with ASP 78 (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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74K LYS* 2.9 51.7 + - - +
75K LYS* 3.4 11.7 + - - +
77K GLU* 1.4 77.9 - - - +
79K GLY* 1.4 57.4 + - - +
81K ILE* 5.1 4.7 - - + -
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Residues in contact with GLY 79 (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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75K LYS 3.4 3.8 + - - -
77K GLU 3.5 0.2 - - - -
78K ASP* 1.4 81.0 - - - +
80K ASN* 1.4 74.8 + - - +
81K ILE* 3.5 10.6 - - - +
125K ARG* 3.6 21.7 - - - +
126K LEU 4.1 1.7 - - - +
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Residues in contact with ASN 80 (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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76K VAL 3.4 13.9 + - - +
77K GLU 4.9 1.1 - - - +
79K GLY* 1.4 78.1 - - - +
81K ILE* 1.4 58.2 + - - +
126K LEU* 2.9 45.3 + - + +
127K THR 3.0 21.3 + - - +
128K ALA* 3.5 21.2 + - - +
130K TYR* 4.3 0.6 - - + -
131K ASP* 4.1 11.3 - - - +
132K ALA* 3.6 27.1 + - + +
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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