Contacts of the strand formed by residues 67 - 72 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59D CYS* 4.4 14.6 - - + -
60D LEU 3.7 13.5 - - - -
61D LEU* 3.9 39.9 - - + +
62D LEU* 5.5 0.2 - - - -
65D SER 4.7 4.5 - - - -
66D GLU* 1.3 81.8 - - - +
68D ILE* 1.3 60.0 + - - +
83D PRO* 3.5 6.1 - - - +
84D LEU* 2.9 50.2 + - + +
85D SER* 4.6 2.8 + - - +
139D PHE* 5.3 0.8 - - - -
464D THR* 4.1 17.9 - - + -
465D LEU 3.4 6.3 + - - -
466D TYR* 3.4 37.2 - + - -
467D GLY* 3.0 26.3 + - - -
693D PHE* 6.4 1.6 - + - -
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Residues in contact with ILE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN 4.1 0.2 - - - +
59D CYS* 3.4 3.2 - - - -
60D LEU* 3.0 52.1 + - + +
62D LEU* 4.0 27.6 - - + -
66D GLU 4.1 0.8 + - - -
67D TYR* 1.3 74.5 - - - +
69D CYS* 1.3 67.3 + - - +
70D TYR* 4.6 5.8 - - + -
81D PHE* 4.2 19.1 - - + -
82D TYR* 3.4 32.8 - - - +
83D PRO* 3.7 9.0 - - + -
91D LYS 5.8 0.2 - - - +
110D ILE* 6.5 0.2 - - + -
117D LEU* 4.6 11.0 - - + -
138D LEU* 4.6 24.2 - - + +
139D PHE* 4.9 5.4 - - + -
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Residues in contact with CYS 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D ASN 3.5 7.2 - - - +
59D CYS* 3.1 27.8 - - - -
68D ILE* 1.3 77.6 - - - +
70D TYR* 1.3 62.2 + - - +
71D HIS* 5.0 2.7 - - + -
80D THR 3.4 0.2 - - - +
81D PHE* 3.2 6.6 - - - -
82D TYR* 2.8 69.5 + - + +
84D LEU* 3.8 14.6 - - - -
481D HIS* 3.4 22.4 - - + -
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Residues in contact with TYR 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D TYR* 3.7 28.8 + + - -
57D SER* 3.1 4.7 - - - -
58D ASN* 3.1 63.4 + - + +
59D CYS 4.6 0.4 - - - -
60D LEU* 4.5 20.2 - - + -
68D ILE* 4.6 7.4 - - + -
69D CYS* 1.3 77.3 - - - +
71D HIS* 1.3 67.5 + - - +
72D PHE* 5.3 0.7 - - + -
79D LEU* 5.1 8.1 - - + -
80D THR 2.9 11.7 - - - +
81D PHE* 3.7 21.8 - + + -
82D TYR* 5.9 0.2 - - - -
108D LEU* 5.1 6.3 - - + -
110D ILE* 3.7 37.8 + - + +
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Residues in contact with HIS 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY* 2.5 40.2 + - - +
56D TYR 3.1 3.8 - - - -
57D SER* 3.1 21.9 - - - -
69D CYS* 5.0 2.2 - - + +
70D TYR* 1.3 79.0 - - - +
72D PHE* 1.3 59.8 + - - +
73D SER 3.8 0.3 + - - -
78D LEU 3.6 1.0 - - - +
79D LEU* 3.4 7.5 - - - +
80D THR* 2.8 39.4 + - - -
82D TYR* 3.9 25.7 + + - -
475D CYS 3.1 26.3 + - - -
476D PHE 3.1 2.2 + - - -
477D GLN 3.5 1.1 - - - -
478D PRO* 3.2 38.3 - - + +
480D ASN 5.6 0.8 + - - -
481D HIS* 5.3 4.0 - - - -
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Residues in contact with PHE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D GLY* 3.9 1.6 - - - -
55D GLU* 3.4 16.7 + - + +
56D TYR* 2.9 27.6 + - + -
70D TYR* 5.3 1.5 - - + -
71D HIS* 1.3 73.4 - - - +
73D SER* 1.3 70.2 + - - +
76D SER* 3.2 43.1 - - - -
78D LEU 3.0 16.2 - - - -
79D LEU* 3.5 18.8 - - + -
97D LEU* 3.8 19.1 - - + -
101D SER* 3.7 23.6 - - - -
104D GLN 4.0 1.1 - - - -
105D ARG* 3.8 28.9 - - + -
108D LEU* 3.7 24.2 - - + -
121D 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