Contacts of the strand formed by residues 67 - 72 (chain A) in PDB entry 3C5E
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 PRO 67 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A PRO 4.4 3.1 - - - +
66A SER* 1.3 89.2 - - - +
68A ALA* 1.3 59.1 + - - +
70A TRP* 5.7 4.3 - - + -
80A MET* 3.9 28.2 - - + -
81A TRP 3.8 6.1 - - - +
83A PHE* 3.6 7.3 - - - -
256A ILE* 6.2 2.7 - - + -
280A GLY 4.6 0.7 - - - +
281A ALA 4.0 0.5 - - - -
282A CYS* 3.3 38.0 + - + +
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Residues in contact with ALA 68 (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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66A SER 3.4 0.6 + - - -
67A PRO* 1.3 75.0 - - - +
69A LEU* 1.3 61.3 + - - +
81A TRP 2.8 11.9 + - - +
82A ASN 4.0 4.5 - - - +
83A PHE* 3.6 39.0 - - + -
86A LEU* 3.7 22.4 - - + -
277A TRP* 2.7 22.3 + - - +
282A CYS* 3.9 5.4 - - - +
283A THR* 2.9 14.7 + - - +
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Residues in contact with LEU 69 (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 ALA* 1.3 81.4 - - + +
70A TRP* 1.3 63.2 + - - +
71A TRP* 4.1 3.6 - - + +
79A LEU 3.8 0.5 - - - +
80A MET* 3.2 6.9 - - - +
81A TRP* 3.0 62.7 + - + -
86A LEU* 4.6 11.0 - - + -
117A PRO* 4.1 16.4 - - + +
120A TRP* 4.1 28.0 - - + -
121A LEU* 5.6 1.1 - - + -
277A TRP* 4.2 7.2 - - + -
282A CYS* 4.3 0.9 - - - -
283A THR* 3.5 23.6 - - + -
285A VAL* 3.7 22.9 - - + -
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Residues in contact with TRP 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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67A PRO* 5.7 3.1 - - + -
69A LEU* 1.3 74.3 - - - +
71A TRP* 1.3 68.7 + - - +
72A VAL* 3.8 8.0 - - + +
78A GLU* 2.8 25.2 + - + +
79A LEU 3.5 12.3 - - - -
80A MET* 4.4 14.1 - - + +
256A ILE* 3.7 33.0 - - + -
282A CYS* 3.9 15.5 - - - -
283A THR 3.0 7.4 + - - +
284A PHE* 3.3 24.7 - + + -
285A VAL* 2.9 25.5 + - - +
303A TYR* 3.6 27.6 - + - -
304A PRO* 4.1 17.7 - - + -
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Residues in contact with TRP 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 LEU* 4.1 4.0 - - + -
70A TRP* 1.3 73.1 - - - +
72A VAL* 1.3 73.8 + - - +
73A ASN* 3.6 31.2 - - + -
77A LYS* 3.9 30.1 - - + -
78A GLU* 3.2 4.2 - - - +
79A LEU* 2.8 62.6 + - + +
81A TRP* 4.8 2.7 - - + -
115A ARG 2.8 27.1 + - - -
116A VAL* 4.5 4.0 - - + -
117A PRO* 3.7 33.9 - - + +
285A VAL* 3.2 30.3 - - + +
287A LEU* 4.1 9.0 - - + +
803A GOL 3.6 28.9 - - - -
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Residues in contact with VAL 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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70A TRP* 3.8 11.7 - - - +
71A TRP* 1.3 88.8 - - - +
73A ASN* 1.3 60.1 + - - +
74A GLY* 4.2 4.5 - - - +
77A LYS 3.5 8.5 - - - +
78A GLU* 3.6 27.1 - - + -
284A PHE* 3.8 23.6 - - + -
285A VAL 2.9 5.5 + - - +
286A HIS* 3.4 34.4 - - + +
287A LEU 2.9 23.9 + - - -
303A TYR* 3.6 17.0 - - + +
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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