Contacts of the strand formed by residues 69 - 74 (chain F) in PDB entry 6FF7
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 VAL 69 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F HIS* 5.0 11.7 - - + -
67F GLY 3.5 3.2 + - - +
68F GLU* 1.3 76.6 - - - +
70F TYR* 1.3 61.3 + - - +
71F CYS 4.8 2.2 - - - +
83F SER* 5.9 4.0 - - - -
84F ALA 4.0 11.2 - - - +
85F GLY* 4.1 1.3 - - - +
331F ASN* 3.6 13.9 - - - +
345F ALA* 4.5 11.1 - - + -
346F SER* 3.3 33.4 + - - +
347F SER* 4.3 0.7 + - - -
349F LYS* 4.9 6.0 - - - +
350F ARG 5.8 1.3 - - - +
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Residues in contact with TYR 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F GLU* 5.1 1.3 - - + +
69F VAL* 1.3 73.7 - - - +
71F CYS* 1.3 64.3 + - - +
84F ALA 3.0 5.9 + - - -
85F GLY* 3.7 5.4 - - - -
86F PHE 5.4 0.2 - - - +
112F VAL 3.8 22.0 - - - +
113F MET* 4.4 10.2 - - - +
331F ASN* 3.6 22.3 - - + +
332F GLU* 3.9 7.9 - - - +
345F ALA* 5.3 1.1 - - - -
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Residues in contact with CYS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69F VAL* 3.6 2.5 - - - +
70F TYR* 1.3 83.8 - - + +
72F CYS* 1.3 64.7 + - - +
83F SER* 3.5 2.3 - - - -
84F ALA* 3.0 31.7 + - + +
112F VAL 5.5 0.4 - - - +
113F MET 4.2 15.9 - - - +
114F GLU* 4.4 1.3 - - + -
115F LEU* 4.2 24.5 - - + +
332F GLU* 4.2 9.2 - - + -
345F ALA* 4.6 5.7 - - - +
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Residues in contact with CYS 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F CYS* 1.3 79.7 - - - +
73F LYS* 1.3 62.1 + - - +
82F ALA 3.1 12.8 - - - +
83F SER* 4.2 9.4 - - - -
115F LEU* 5.5 3.4 - - - -
332F GLU* 4.4 11.5 - - + +
334F ALA* 4.0 14.4 - - + +
343F ILE* 5.3 14.8 - - + +
345F ALA* 4.1 18.2 - - + +
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Residues in contact with LYS 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F CYS* 1.3 75.8 - - - +
74F PHE* 1.3 65.0 + - - +
81F LEU* 3.4 6.6 - - - +
82F ALA* 2.8 38.4 + - + +
115F LEU* 4.7 22.4 - - + +
116F HIS* 5.1 6.3 - - - -
117F TYR* 5.2 6.1 - - + +
334F ALA* 4.6 7.6 - - - -
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Residues in contact with PHE 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LYS* 1.3 80.2 - - - +
75F HIS* 1.3 69.9 + - - +
76F PRO* 3.5 1.9 - - - +
78F GLY* 5.7 3.4 - - - -
80F THR 3.8 5.2 - - - +
81F LEU* 4.6 2.0 - - + +
117F TYR* 4.9 6.7 - - - +
334F ALA* 4.9 6.5 - - + +
335F PHE 4.3 19.1 - - - +
336F HIS* 4.6 11.2 - - + +
337F PRO* 5.2 3.1 - - + -
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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