Contacts of the strand formed by residues 77 - 83 (chain D) in PDB entry 2W2X
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 PHE 77 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 5.2 5.6 - - + -
64A TYR* 4.8 15.3 - + - -
75D LYS* 3.5 1.0 - - - +
76D SER* 1.3 96.6 - - - +
78D VAL* 1.3 61.0 + - - +
94D ALA* 3.1 5.6 - - - +
95D THR* 3.0 46.4 + - - +
96D ASP 3.2 28.3 - - - -
98D VAL* 3.3 46.2 - - + -
101D LEU* 3.5 28.1 - - + +
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Residues in contact with VAL 78 (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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22D TRP* 4.5 8.5 - - + -
67D LYS* 3.9 3.8 - - - +
68D ALA* 3.0 36.3 + - + +
71D GLY* 3.2 33.8 - - - -
72D LYS* 3.4 22.7 - - + +
75D LYS* 3.8 9.6 - - + +
76D SER 3.7 1.0 + - - -
77D PHE* 1.3 76.7 - - - +
79D PHE* 1.3 69.6 + - - +
80D ILE* 4.3 10.1 - - + -
92D GLU* 5.1 2.2 - - + -
93D PHE 3.2 17.0 - - - +
94D ALA* 4.2 4.9 - - + -
101D LEU* 3.8 8.1 - - - +
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Residues in contact with PHE 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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12D LEU* 4.4 16.8 - - + -
34D LEU* 5.4 0.9 - - + -
65D VAL* 3.6 20.0 - - + -
66D VAL 3.2 12.8 - - - +
67D LYS* 4.3 4.5 - - - -
78D VAL* 1.3 74.3 - - - +
80D ILE* 1.3 69.4 + - - +
81D LEU* 3.6 15.0 - - + -
91D VAL 4.1 0.2 - - - +
92D GLU* 3.8 0.2 - - - -
93D PHE* 2.9 66.2 + + + +
94D ALA* 5.1 0.7 - - - -
95D THR* 5.2 2.9 - - + -
101D LEU* 3.9 21.5 - - + -
104D TRP* 3.9 23.6 - + + -
105D PHE* 4.4 9.0 - + + -
108D ILE* 3.3 30.7 - - + -
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Residues in contact with ILE 80 (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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64D ASN 3.4 2.8 - - - +
65D VAL* 3.5 2.3 - - - -
66D VAL* 2.7 43.7 + - + +
68D ALA* 5.2 7.9 - - + +
72D LYS* 4.0 30.1 - - + -
78D VAL* 4.3 7.6 - - + -
79D PHE* 1.3 80.4 - - - +
81D LEU* 1.3 71.7 + - - +
82D GLU* 3.5 32.1 + - + +
90D PRO* 4.1 13.7 - - + -
91D VAL 3.5 8.3 - - - +
92D GLU* 3.7 20.6 - - + +
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Residues in contact with LEU 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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34D LEU* 4.6 5.2 - - + -
58D LEU* 3.5 30.7 - - + -
60D LEU* 3.9 24.7 - - + -
63D TYR* 3.5 26.4 - - + -
64D ASN 3.6 4.0 - - - +
65D VAL* 4.2 11.2 - - + -
79D PHE* 3.6 30.3 - - + -
80D ILE* 1.3 73.6 - - - +
82D GLU* 1.3 62.5 + - - +
90D PRO* 3.2 7.3 - - - +
91D VAL* 2.9 33.2 + - + +
93D PHE* 3.7 12.1 - - + -
108D ILE* 4.2 9.9 - - + -
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Residues in contact with GLU 82 (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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63D TYR* 3.8 1.1 - - - -
64D ASN* 2.9 41.3 + - + +
66D VAL* 3.3 39.8 - - + +
80D ILE* 3.5 23.4 + - + +
81D LEU* 1.3 70.8 - - - +
83D PRO* 1.4 74.4 - - + +
90D PRO* 4.8 4.3 - - + -
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Residues in contact with PRO 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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62D THR 3.6 2.2 - - - +
63D TYR* 3.6 15.7 - - + -
64D ASN* 5.3 0.2 - - - +
81D LEU 3.9 3.8 - - - +
82D GLU* 1.4 88.9 - - + +
84D LYS* 1.3 62.1 + - - +
85D GLN 4.2 11.6 - - - +
88D ASP* 3.4 47.6 - - + +
89D PRO 3.6 15.3 - - - +
90D PRO* 3.9 11.9 - - + -
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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