Contacts of the strand formed by residues 89 - 94 (chain B) in PDB entry 6DDE
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 LYS 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ALA* 4.5 2.3 - - - +
15A ARG* 5.1 3.8 - - - +
16A SER* 2.4 39.4 + - - +
19A ILE* 3.6 33.2 - - + -
20A ASP* 3.5 24.6 + - + +
23A LEU* 4.3 5.8 - - + -
52B ARG 3.8 7.7 + - - -
53B GLY* 3.7 14.1 - - - -
80B ILE* 3.9 15.9 - - + -
81B ILE 3.8 8.5 - - - +
82B TRP* 3.5 37.8 - - + +
87B THR 5.1 2.0 + - - -
88B ASN* 1.3 78.7 - - - +
90B VAL* 1.3 67.4 + - - +
91B HIS 4.8 2.5 - - - +
102E TYR* 5.3 1.0 - - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ARG* 3.3 24.9 + - - +
19A ILE* 5.5 3.3 - - - +
69B LEU* 4.2 11.2 - - + -
81B ILE* 3.1 31.1 + - + +
82B TRP 4.1 6.1 - - - +
83B ASP* 4.9 7.9 - - + +
88B ASN* 5.9 1.1 - - + -
89B LYS* 1.3 79.9 - - - +
91B HIS* 1.3 89.3 + - + +
102E TYR* 3.8 31.9 - - + -
103E TYR* 4.0 20.6 - - + +
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Residues in contact with HIS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ARG* 3.9 13.9 + - - +
19A ILE* 4.6 6.8 - - - +
80B ILE* 3.2 6.8 - - - +
81B ILE* 2.9 53.3 + - + +
89B LYS* 3.9 1.1 - - - +
90B VAL* 1.3 105.9 + - + +
92B ALA* 1.3 60.1 + - - +
93B ILE* 3.8 11.2 - - + -
126B LEU* 4.6 19.7 + - + +
127B LYS* 5.5 3.0 + - - -
132B ASN* 5.8 2.9 - - - +
133B VAL* 3.5 28.1 + - + +
102E TYR* 3.8 33.3 + + - -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.8 31.7 - - + +
22A ASN* 6.3 1.1 - - + -
23A LEU* 4.1 16.4 - - + -
78B LYS* 5.2 4.7 + - + +
79B LEU 3.8 0.2 - - - -
80B ILE* 3.7 22.0 - - + -
91B HIS* 1.3 73.3 - - - +
93B ILE* 1.3 63.7 + - - +
94B PRO* 3.3 9.7 - - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B GLY 4.0 0.2 - - - +
78B LYS* 3.9 4.9 - - - -
79B LEU* 2.9 54.7 + - + +
81B ILE* 4.1 8.3 - - + -
91B HIS* 4.2 9.0 - - + -
92B ALA* 1.3 70.8 - - - +
94B PRO* 1.3 76.8 - - + +
95B LEU* 3.8 1.0 + - - +
112B VAL* 4.3 2.2 - - + -
124B TYR* 3.6 35.0 - - + -
126B LEU* 3.8 29.4 - - + -
133B VAL* 3.7 32.3 - - + -
135B VAL* 6.1 1.8 - - + -
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Residues in contact with PRO 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B LYS* 3.2 28.9 - - - +
92B ALA 3.3 9.6 - - - +
93B ILE* 1.3 98.4 - - + +
95B LEU* 1.3 62.1 + - - +
124B TYR* 4.4 2.6 + - - -
132B ASN* 6.3 1.8 - - - +
133B VAL* 4.9 7.2 - - + -
135B VAL* 5.4 5.4 - - - +
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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
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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