Contacts of the helix formed by residues 69 - 76 (chain B) in PDB entry 6W01
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B VAL 3.4 0.8 + - - -
68B PRO* 1.3 75.5 - - - +
70B VAL* 1.3 66.6 + - - +
71B LYS* 3.5 20.4 - - + -
72B ILE* 2.9 23.2 + - + +
73B LEU* 3.3 8.5 + - - +
90B LYS* 4.4 8.7 + - - -
158B PRO* 6.1 0.3 - - - +
160B GLN* 3.5 13.9 + - + +
161B ALA* 4.7 4.8 - - - +
162B SER* 4.5 17.2 - - - +
167B THR* 3.0 33.1 + - + +
198B SER* 2.4 34.6 + - - -
273B ASP* 3.8 13.4 - - - +
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Residues in contact with VAL 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO 3.6 1.3 + - - +
69B GLU* 1.3 73.6 - - - +
71B LYS* 1.3 58.5 + - - +
73B LEU* 3.2 9.0 + - + +
74B ASN* 2.8 51.6 + - - +
86B ILE* 4.4 12.3 - - + -
87B TRP 4.6 1.6 - - - +
88B ASP* 3.6 45.3 - - + +
89B TYR 5.5 0.2 - - - +
95B ALA* 4.2 19.7 - - + +
273B ASP* 3.4 16.1 + - + +
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Residues in contact with LYS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B GLU* 3.5 18.4 + - + -
70B VAL* 1.3 77.5 - - - +
72B ILE* 1.3 65.8 + - + +
74B ASN* 3.6 4.6 + - - +
75B ASN* 2.9 37.7 + - - +
160B GLN* 5.3 0.4 - - - +
196B THR* 2.8 29.4 + - - -
198B SER* 3.0 34.5 + - - +
273B ASP* 2.9 36.2 + - - +
274B SER* 4.0 32.4 + - - +
275B THR* 4.2 5.3 + - - +
324B ASP* 3.9 16.2 - - - +
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Residues in contact with ILE 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 4.5 2.2 - - + -
69B GLU* 2.9 22.8 + - + +
71B LYS* 1.3 84.6 - - + +
73B LEU* 1.3 65.7 + - - +
75B ASN* 3.2 4.8 + - - +
76B LEU* 3.0 30.3 + - + +
158B PRO* 4.3 23.8 - - + -
179B TYR* 3.6 37.9 - - + +
195B PHE* 4.5 3.8 - - + -
324B ASP* 3.7 42.2 - - + +
325B TYR* 4.2 8.7 - - + -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PRO* 3.6 32.3 - - + +
69B GLU 3.8 9.0 - - - +
70B VAL* 3.2 11.1 + - + +
72B ILE* 1.3 76.9 - - - +
74B ASN* 1.3 64.2 + - - +
76B LEU* 3.2 4.6 + - + -
77B GLY 3.1 4.7 + - - -
78B VAL* 3.0 43.9 + - + +
86B ILE* 3.9 38.6 - - + -
95B ALA* 5.6 0.4 - - + -
96B HIS* 4.4 13.7 - - + +
123B PHE* 3.7 30.5 - - + -
142B VAL* 5.2 2.0 - - + -
179B TYR* 5.1 6.5 - - + -
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Residues in contact with ASN 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B VAL* 2.8 43.2 + - - +
71B LYS* 3.8 5.4 - - - +
73B LEU* 1.3 74.1 - - - +
75B ASN* 1.3 66.3 + - - +
77B GLY* 3.0 7.1 + - - -
78B VAL 5.0 0.9 - - - +
95B ALA 5.2 3.8 - - - +
96B HIS* 5.0 8.0 + - - -
272B MET* 4.5 14.3 - - - +
273B ASP 4.3 13.1 + - - -
404B EDO 2.8 38.1 + - - +
411B PEG 5.4 0.2 - - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B LYS* 2.9 25.4 + - - +
72B ILE 3.2 3.8 + - - +
74B ASN* 1.3 79.6 - - - +
76B LEU* 1.3 58.4 + - - +
77B GLY 3.3 0.4 - - - -
275B THR* 2.9 27.6 + - - -
324B ASP* 2.9 33.4 + - - +
325B TYR* 4.6 1.5 - - + +
326B THR* 3.6 26.2 + - - +
403B EDO 4.0 22.3 + - - -
411B PEG 2.9 25.8 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE* 3.0 25.8 + - + +
73B LEU* 3.8 6.3 - - + +
74B ASN 3.1 0.4 - - - -
75B ASN* 1.3 74.9 - - - +
77B GLY* 1.3 58.1 + - - +
78B VAL* 3.4 2.1 + - + -
142B VAL* 4.0 28.2 - - + +
179B TYR* 3.5 38.4 - - + -
181B LYS* 2.7 31.0 + - + +
190B LEU* 3.7 25.1 - - + -
325B TYR* 3.6 35.0 - - + -
411B PEG 3.3 13.7 - - - +
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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