Contacts of the strand formed by residues 73 - 77 (chain D) in PDB entry 6Q3W
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 73 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72D LEU* 1.3 72.3 - - - +
74D SER* 1.3 59.4 + - - +
75D LEU* 5.7 0.4 - - - -
88D LEU 4.2 1.2 - - - +
89D GLN* 3.2 2.9 - - - -
90D PHE* 2.6 52.7 + - + +
91D PRO 5.0 3.3 - - - +
92D LEU* 6.1 2.2 - - + -
114D ILE* 4.7 13.9 - - + -
124D GLY* 5.5 1.1 - - - -
125D PHE* 3.3 28.3 - - + +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D LEU 4.0 1.0 + - - -
73D VAL* 1.3 73.9 - - - +
75D LEU* 1.3 62.7 + - - +
89D GLN* 3.9 18.8 - - - +
125D PHE* 3.1 8.8 + - - +
126D SER* 3.3 16.1 - - - -
127D ALA* 3.0 25.6 + - - +
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Residues in contact with LEU 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D VAL 5.7 0.4 - - - -
74D SER* 1.3 76.8 - - - +
76D LEU* 1.3 62.2 + - - +
77D THR* 5.5 6.1 - - + -
86D GLN 5.3 0.2 - - - -
87D ARG* 3.3 24.6 - - - +
88D LEU 3.6 17.0 + - - +
89D GLN 4.8 0.2 - - - +
107D ALA* 6.4 1.8 - - + -
110D VAL* 6.1 6.1 - - + -
125D PHE* 6.0 2.5 - - + -
127D ALA* 3.2 15.5 - - + +
129D VAL* 6.2 2.2 - - + +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 1.3 77.2 - - - +
77D THR* 1.3 75.2 + - - +
78D THR* 4.9 3.6 - - - +
86D GLN* 3.1 26.7 - - + +
87D ARG* 4.8 6.7 - - + -
127D ALA 3.0 9.6 + - - +
128D VAL* 3.3 25.6 - - + +
129D VAL* 2.9 22.8 + - - +
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Residues in contact with THR 77 (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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75D LEU* 5.5 5.4 - - + -
76D LEU* 1.3 92.8 - - - +
78D THR* 1.3 76.5 + - - +
86D GLN* 3.8 26.4 + - - +
106D TRP* 4.5 23.9 - - + +
107D ALA* 5.6 5.4 - - + +
128D VAL* 5.7 0.2 - - - -
129D VAL* 3.2 22.4 - - + -
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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
------------------------------------------------------------
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