Contacts of the strand formed by residues 77 - 83 (chain D) in PDB entry 3BRW
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 GLY 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5D LYS 3.4 4.1 + - - +
6D LEU* 3.5 16.3 - - - +
7D VAL* 2.9 26.9 + - - +
76D GLN* 1.3 79.5 - - - +
78D PHE* 1.3 66.3 + - - -
110D PRO* 3.4 15.9 - - - -
161D LEU* 4.1 9.8 - - - +
165D ILE* 4.2 1.1 - - - +
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Residues in contact with PHE 78 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D VAL* 3.3 39.0 - - + +
9D LEU* 4.4 3.8 - - + -
71D TYR 3.8 7.0 - - - -
72D MET* 3.5 27.1 - - - -
75D GLY* 3.6 21.1 - - - -
76D GLN 4.3 1.1 - - - -
77D GLY* 1.3 72.8 - - - -
79D ALA* 1.3 59.9 - - - +
80D LEU* 3.8 19.9 + - + +
100D ILE* 3.7 28.7 - - + -
104D LYS* 3.7 21.1 - - - -
109D VAL* 3.9 19.5 - - + -
110D PRO 2.8 12.7 + - - +
111D MET* 3.5 7.6 - - - -
112D ILE* 2.9 27.9 + - - +
161D LEU* 3.8 5.8 - - - +
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Residues in contact with ALA 79 (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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7D VAL 2.9 8.2 + - - +
8D VAL* 3.5 24.3 - - + +
9D LEU* 2.9 31.0 + - - +
78D PHE* 1.3 70.7 - - - +
80D LEU* 1.3 62.4 + - - +
81D VAL* 3.7 1.7 + - + -
112D ILE* 3.4 20.6 - - + -
114D VAL* 4.5 5.4 - - + -
157D ILE* 4.2 16.4 - - + -
158D PHE* 5.4 2.0 - - + -
161D LEU* 4.2 6.8 - - + +
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Residues in contact with LEU 80 (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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9D LEU* 3.4 31.0 - - + -
78D PHE* 3.9 10.8 - - + +
79D ALA* 1.3 71.9 - - - +
81D VAL* 1.3 61.5 + - - +
93D LEU* 4.0 17.9 - - + +
96D LEU* 4.9 1.8 - - + -
97D ARG* 3.8 25.1 - - + +
100D ILE* 4.9 3.8 - - + -
111D MET* 3.5 28.0 - - + -
112D ILE 2.8 12.5 + - - +
113D LEU* 3.6 13.5 - - + +
114D VAL 2.9 23.4 + - - -
138D TRP* 3.6 33.4 - - + -
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Residues in contact with VAL 81 (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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8D VAL* 3.7 29.2 - - + -
9D LEU 2.9 9.4 + - - +
10D GLY* 3.6 13.5 - - - -
11D SER 4.3 1.0 + - - -
14D VAL* 3.8 25.9 - - + +
16D LYS* 4.3 3.4 - - + -
19D LEU* 4.0 11.9 - - + -
79D ALA* 4.0 4.7 - - + +
80D LEU* 1.3 76.2 - - - +
82D TYR* 1.3 72.3 + - - +
89D THR 4.7 0.9 - - - +
93D LEU* 3.6 12.6 - - - +
114D VAL* 3.4 30.5 - - + +
116D ASN* 3.8 17.3 - - + -
157D ILE* 6.3 0.4 - - + -
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Residues in contact with TYR 82 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D VAL* 3.8 12.8 - - - -
81D VAL* 1.3 74.3 - - - +
83D SER* 1.3 73.5 + - - +
84D ILE* 4.1 9.2 - - + +
89D THR 3.6 20.0 - - - +
90D PHE* 3.5 38.6 - + + -
93D LEU* 3.6 19.5 - - + -
113D LEU* 4.1 16.2 - - + -
114D VAL 3.0 11.1 + - - +
115D GLY* 3.4 28.3 - - - -
116D ASN* 2.9 29.8 + - - +
126D VAL* 3.6 17.4 - - + +
127D GLY 4.7 2.6 + - - -
131D GLY* 3.7 11.3 + - - -
143D PHE* 3.5 20.7 - + - -
145D GLU* 5.0 1.4 + - - +
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Residues in contact with SER 83 (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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13D GLY 5.1 0.2 - - - -
14D VAL* 3.6 20.8 - - - +
82D TYR* 1.3 86.9 - - - +
84D ILE* 1.3 58.0 + - - +
85D THR* 2.9 28.2 + - - -
86D ALA* 3.2 22.8 - - - +
89D THR* 3.2 12.9 + - - -
116D ASN 3.8 5.2 - - - -
117D LYS* 3.3 22.7 + - - +
126D VAL* 3.5 2.6 - - - +
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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