Contacts of the helix formed by residues 71 - 82 (chain Q) 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 SER 71 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13Q ASP 4.7 15.7 + - - -
14Q GLY 5.6 0.4 - - - +
64Q PHE* 5.4 0.9 - - - +
69Q ALA 3.8 1.0 + - - -
70Q ILE* 1.3 79.9 - - - +
72Q ARG* 1.3 66.2 + - - +
73Q GLU* 3.4 8.7 - - - -
74Q LEU* 3.9 7.7 + - - +
75Q TYR* 3.3 21.7 + - - +
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Residues in contact with ARG 72 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q SER* 1.3 75.5 - - - +
73Q GLU* 1.3 60.3 + - - +
75Q TYR* 3.3 8.5 + - - +
76Q GLU* 2.9 30.1 + - - +
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Residues in contact with GLU 73 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71Q SER* 3.4 5.7 - - - -
72Q ARG* 1.3 78.6 - - - +
74Q LEU* 1.3 57.1 + - - +
76Q GLU* 3.4 6.8 + - - +
77Q TYR* 2.9 26.8 + - - +
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Residues in contact with LEU 74 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 6.1 3.6 - - + -
12Q PRO* 4.9 12.3 - - + +
13Q ASP 4.6 16.2 - - - +
14Q GLY 5.2 4.7 - - - +
15Q TRP* 6.3 1.3 - - + -
70Q ILE* 5.7 5.2 - - + -
71Q SER* 3.9 11.9 + - - +
73Q GLU* 1.3 76.2 - - - +
75Q TYR* 1.3 59.7 + - - +
77Q TYR* 3.4 9.7 - - + +
78Q CYS* 2.9 30.0 + - - +
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Residues in contact with TYR 75 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64Q PHE* 4.6 19.7 - - + -
70Q ILE* 5.8 2.6 - - + +
71Q SER 3.3 20.6 + - - +
72Q ARG* 3.4 9.4 - - - +
73Q GLU 3.2 0.4 - - - -
74Q LEU* 1.3 75.7 - - - +
76Q GLU* 1.3 57.0 + - - +
78Q CYS* 3.3 6.8 + - - +
79Q ILE* 3.0 27.5 + - - +
84Q ALA* 5.6 1.0 - - - +
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Residues in contact with GLU 76 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72Q ARG 2.9 16.7 + - - +
73Q GLU* 3.8 5.8 - - - +
75Q TYR* 1.3 76.1 - - - +
77Q TYR* 1.3 57.5 + - - +
79Q ILE* 3.4 7.6 + - - +
80Q LYS* 2.9 30.9 + - - +
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Residues in contact with TYR 77 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Q PRO* 5.6 9.6 - - + -
73Q GLU 2.9 18.1 + - - +
74Q LEU* 3.4 12.3 - - + +
76Q GLU* 1.3 77.9 - - - +
78Q CYS* 1.3 56.3 + - - +
80Q LYS* 3.8 5.0 - - - +
81Q GLU* 2.9 31.6 + - - +
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Residues in contact with CYS 78 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60Q ILE* 5.6 7.2 - - + -
74Q LEU 2.9 16.3 + - - +
75Q TYR* 3.3 6.7 + - - +
77Q TYR* 1.3 73.7 - - - +
79Q ILE* 1.3 64.0 + - - +
81Q GLU* 4.0 4.0 - - - +
82Q GLY 3.4 1.4 + - - -
83Q TYR* 3.0 43.0 + - + -
84Q ALA* 3.1 11.2 + - + -
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Residues in contact with ILE 79 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Q TYR 3.0 16.5 + - - +
76Q GLU* 3.7 8.7 - - - +
77Q TYR 3.3 0.4 - - - -
78Q CYS* 1.3 78.8 - - - +
80Q LYS* 1.3 62.5 + - - +
81Q GLU 3.5 0.3 + - - -
82Q GLY* 3.7 5.0 + - - -
84Q ALA* 3.4 25.1 - - + +
85Q ASP 4.2 18.2 - - - +
86Q LYS* 5.3 7.2 - - + +
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Residues in contact with LYS 80 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76Q GLU 2.9 18.8 + - - +
77Q TYR* 3.3 6.5 + - - +
79Q ILE* 1.3 78.8 - - - +
81Q GLU* 1.3 60.4 + - - +
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Residues in contact with GLU 81 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q LYS* 4.7 14.8 - - - +
77Q TYR 2.9 17.6 + - - +
78Q CYS* 4.4 4.5 - - - +
80Q LYS* 1.3 79.5 - - - +
82Q GLY* 1.3 58.0 + - - +
83Q TYR* 4.7 3.6 - - + +
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Residues in contact with GLY 82 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Q CYS 3.4 3.4 + - - -
79Q ILE 3.7 5.5 + - - -
80Q LYS 3.5 1.8 - - - -
81Q GLU* 1.3 80.0 - - - +
83Q TYR* 1.3 66.0 + - - +
84Q ALA 3.2 8.7 + - - +
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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