Contacts of the helix formed by residues 69 - 76 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A VAL 3.4 1.4 + - - -
68A PRO* 1.3 75.7 - - - +
70A VAL* 1.3 66.3 + - - +
71A LYS* 3.6 19.8 + - + -
72A ILE* 3.0 24.1 + - + +
73A LEU* 3.3 9.2 + - - +
90A LYS* 4.3 12.6 + - - -
158A PRO* 6.1 0.7 - - - +
160A GLN* 3.6 14.0 + - + +
161A ALA* 4.6 4.8 - - - +
162A SER* 4.4 19.3 - - - +
167A THR* 2.9 31.7 + - + +
198A SER* 2.5 32.6 + - - -
273A ASP* 3.8 10.7 - - - +
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Residues in contact with VAL 70 (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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68A PRO 4.4 0.7 - - - +
69A GLU* 1.3 73.1 - - - +
71A LYS* 1.3 63.8 + - - +
73A LEU* 3.1 9.2 + - + +
74A ASN* 2.9 46.5 + - - +
86A ILE* 4.2 14.4 - - + -
87A TRP 4.6 1.6 - - - +
88A ASP* 3.6 42.0 - - + +
89A TYR 5.5 0.2 - - - +
95A ALA* 4.0 24.2 - - + +
96A HIS* 6.2 0.2 - - - +
273A ASP* 3.3 16.2 + - + +
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Residues in contact with LYS 71 (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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69A GLU* 3.6 21.1 + - + -
70A VAL* 1.3 76.6 - - - +
72A ILE* 1.3 66.3 + - + +
74A ASN* 3.8 4.9 - - - +
75A ASN* 2.9 38.0 + - - +
160A GLN* 5.3 0.7 - - - +
196A THR* 2.9 26.7 + - - +
198A SER* 2.8 35.1 + - - +
273A ASP* 2.9 36.1 + - - +
274A SER* 3.9 32.6 + - - +
275A THR* 4.1 4.6 + - - +
324A ASP* 3.9 15.9 - - - +
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Residues in contact with ILE 72 (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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68A PRO* 4.6 2.2 - - + -
69A GLU* 3.0 22.1 + - + +
71A LYS* 1.3 84.1 - - + +
73A LEU* 1.3 66.2 + - - +
75A ASN* 3.3 4.9 + - - +
76A LEU* 3.0 29.3 + - + +
158A PRO* 4.3 24.0 - - + -
179A TYR* 3.5 37.5 - - + +
195A PHE* 4.4 5.6 - - + -
324A ASP* 3.7 42.6 - - + +
325A TYR* 4.3 6.7 - - + -
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Residues in contact with LEU 73 (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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68A PRO* 3.7 31.4 - - + +
69A GLU 3.3 8.3 + - - +
70A VAL* 3.1 12.2 + - + +
72A ILE* 1.3 75.8 - - - +
74A ASN* 1.3 62.4 + - - +
76A LEU* 3.2 4.0 + - + -
77A GLY 3.1 4.3 + - - -
78A VAL* 2.9 47.9 + - + +
86A ILE* 3.9 38.4 - - + -
95A ALA* 5.5 0.2 - - + -
96A HIS* 4.4 13.5 - - + +
123A PHE* 3.8 29.8 - - + -
142A VAL* 5.2 4.0 - - + -
179A TYR* 5.2 3.4 - - + -
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Residues in contact with ASN 74 (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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70A VAL* 2.9 40.7 + - - +
71A LYS* 3.8 4.7 - - - +
73A LEU* 1.3 80.4 - - - +
75A ASN* 1.3 61.3 + - - +
77A GLY* 2.9 16.1 + - - -
78A VAL 4.9 0.4 - - - +
95A ALA 5.1 3.8 - - - +
96A HIS* 4.9 8.8 + - - -
272A MET* 4.9 11.1 - - - +
273A ASP 4.3 12.3 + - - -
406A PEG 4.7 2.1 + - - -
407A EDO 3.5 35.5 + - - +
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Residues in contact with ASN 75 (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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71A LYS* 2.9 25.3 + - - +
72A ILE 3.3 2.9 + - - +
74A ASN* 1.3 80.2 - - - +
76A LEU* 1.3 59.0 + - - +
77A GLY 3.2 0.7 - - - -
274A SER* 6.2 0.2 - - - -
275A THR* 3.0 28.9 + - - -
324A ASP* 2.9 34.3 + - - +
325A TYR* 4.7 1.9 - - + +
326A THR* 3.5 31.6 + - - +
406A PEG 2.9 27.2 - - - +
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Residues in contact with LEU 76 (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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72A ILE* 3.0 26.2 + - + +
73A LEU* 3.8 5.8 - - + +
74A ASN 3.1 0.6 - - - -
75A ASN* 1.3 76.3 - - - +
77A GLY* 1.3 61.5 + - - +
78A VAL* 3.4 2.1 + - + -
121A THR* 4.4 0.3 - - - +
142A VAL* 4.0 23.5 - - + +
179A TYR* 3.5 39.9 - - + -
181A LYS* 3.2 29.3 + - + -
190A LEU* 3.9 24.7 - - + -
325A TYR* 3.7 34.5 - - + -
406A PEG 3.4 13.5 - - - +
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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