Contacts of the strand formed by residues 67 - 72 (chain C) in PDB entry 3F7F
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 TYR 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59C CYS* 4.4 14.6 - - + -
60C LEU 3.7 13.5 - - - -
61C LEU* 3.9 41.4 - - + +
62C LEU* 5.5 0.2 - - - -
65C SER 4.7 4.7 - - - -
66C GLU* 1.3 82.0 - - - +
68C ILE* 1.3 60.3 + - - +
83C PRO* 3.5 6.2 - - - +
84C LEU* 2.9 48.9 + - + +
85C SER* 4.6 2.9 + - - +
139C PHE* 5.3 0.8 - - - -
464C THR* 4.1 18.2 - - + -
465C LEU 3.5 6.1 + - - -
466C TYR* 3.4 37.6 - + - -
467C GLY* 3.0 25.7 + - - -
693C PHE* 6.4 1.6 - + - -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASN 4.1 0.2 - - - +
59C CYS* 3.4 2.8 - - - -
60C LEU* 3.0 52.5 + - + +
62C LEU* 4.0 27.4 - - + -
66C GLU 4.2 0.8 + - - -
67C TYR* 1.3 74.3 - - - +
69C CYS* 1.3 67.7 + - - +
70C TYR* 4.6 5.5 - - + -
81C PHE* 4.2 19.3 - - + -
82C TYR* 3.4 31.6 - - - +
83C PRO* 3.7 9.0 - - + -
91C LYS 5.8 0.2 - - - +
110C ILE* 6.5 0.2 - - + -
117C LEU* 4.6 10.5 - - + -
138C LEU* 4.6 24.7 - - + +
139C PHE* 4.9 5.4 - - + -
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Residues in contact with CYS 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C ASN 3.5 6.7 - - - +
59C CYS* 3.0 28.7 - - - -
68C ILE* 1.3 77.5 - - - +
70C TYR* 1.3 62.4 + - - +
71C HIS* 5.0 2.7 - - + -
80C THR 3.4 0.2 - - - +
81C PHE* 3.2 6.6 - - - -
82C TYR* 2.7 68.1 + - + +
84C LEU* 3.8 15.5 - - - -
481C HIS* 3.4 22.2 - - + -
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Residues in contact with TYR 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C TYR* 3.7 28.7 + + - -
57C SER* 3.1 4.9 - - - -
58C ASN* 3.1 63.1 + - + +
59C CYS 4.5 0.4 - - - -
60C LEU* 4.5 20.2 - - + -
68C ILE* 4.6 7.4 - - + -
69C CYS* 1.3 77.3 - - - +
71C HIS* 1.3 66.6 + - - +
72C PHE* 5.3 0.9 - - + -
79C LEU* 5.0 7.6 - - + -
80C THR 2.9 12.1 - - - +
81C PHE* 3.7 21.8 - + + -
108C LEU* 5.1 6.3 - - + -
110C ILE* 3.7 36.7 + - + +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLY* 2.5 39.8 + - - +
56C TYR 3.1 3.8 - - - -
57C SER* 3.1 19.4 - - - -
69C CYS* 5.0 2.2 - - + +
70C TYR* 1.3 79.2 - - - +
72C PHE* 1.3 60.3 + - - +
73C SER 3.8 0.3 + - - -
78C LEU 3.6 1.2 - - - +
79C LEU* 3.4 7.1 - - - -
80C THR* 2.9 39.8 + - - -
82C TYR* 3.9 25.5 + + - -
475C CYS 3.1 26.5 + - - -
476C PHE 3.1 1.9 + - - -
477C GLN 3.4 1.1 - - - -
478C PRO* 3.1 38.2 - - + +
480C ASN 5.6 0.8 + - - -
481C HIS* 5.3 4.2 - - - -
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Residues in contact with PHE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C GLY* 3.9 1.4 - - - -
55C GLU* 3.4 17.4 + - + +
56C TYR* 2.9 28.1 + - + +
70C TYR* 5.3 1.5 - - + -
71C HIS* 1.3 73.0 - - - +
73C SER* 1.3 69.5 + - - +
76C SER* 3.3 42.8 - - - -
78C LEU 3.0 15.9 - - - -
79C LEU* 3.5 19.1 - - + -
97C LEU* 3.8 19.3 - - + -
101C SER* 3.7 23.6 - - - -
104C GLN 4.0 1.3 - - - -
105C ARG* 3.8 28.9 - - + -
108C LEU* 3.7 25.1 - - + -
121C VAL* 4.7 0.9 - - + -
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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