Contacts of the strand formed by residues 90 - 95 (chain A) in PDB entry 3H3B
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 TYR 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A TYR* 3.7 1.4 - - - +
85A LEU* 3.5 8.2 - - - +
86A PHE* 2.8 52.1 + - + +
87A GLU* 4.7 9.6 - - + -
89A ASN* 1.3 92.4 + - + +
91A ALA* 1.3 62.4 + - - +
92A LEU 4.1 9.9 - - - +
93A ALA* 4.8 0.7 - - + -
130A GLY 3.5 20.9 - - - +
131A VAL 3.9 14.1 - - - -
132A LEU* 3.6 42.0 - - + -
159A LEU* 4.0 27.5 - - + +
161A LEU* 3.4 26.3 - - + +
204D PHE 4.0 4.9 + - - -
205D THR* 3.9 10.7 - - - +
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Residues in contact with ALA 91 (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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61A TYR* 3.3 8.3 - - - -
62A VAL 2.7 32.3 + - - -
80A VAL* 3.7 19.1 - - + +
82A GLY* 4.4 2.2 - - - -
85A LEU* 3.7 7.3 - - + +
86A PHE* 6.0 0.2 - - - -
90A TYR* 1.3 73.6 - - - +
92A LEU* 1.3 56.3 + - + +
126A ILE* 3.7 21.1 - - + -
128A LYS 3.2 26.5 - - - +
129A GLY 4.1 0.7 - - - -
130A GLY 3.0 9.6 + - - +
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Residues in contact with LEU 92 (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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62A VAL* 3.5 30.7 - - + +
64A ILE* 4.6 1.1 - - + -
80A VAL* 5.8 4.0 - - + -
90A TYR* 4.1 2.4 - - - +
91A ALA* 1.3 80.1 - - - +
93A ALA* 1.3 62.3 + - - +
94A VAL* 4.0 20.4 - - + -
118A LEU* 4.4 11.9 - - + -
120A LEU* 4.4 17.3 - - + -
123A LEU* 4.9 5.6 - - + -
126A ILE* 4.8 7.6 - - + -
130A GLY 3.2 8.0 + - - +
131A VAL* 3.4 27.8 - - + -
132A LEU* 2.8 31.7 + - - +
133A ILE* 5.4 0.4 - - + -
147A TRP* 4.0 21.8 - - + -
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Residues in contact with ALA 93 (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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62A VAL 3.0 10.8 + - - +
63A LEU* 3.5 12.2 - - + +
64A ILE 2.9 27.5 + - - +
86A PHE* 3.7 35.2 - - + -
90A TYR* 4.8 1.3 - - + -
92A LEU* 1.3 75.3 - - - +
94A VAL* 1.3 63.1 + - - +
95A LEU* 4.0 3.6 - - + -
132A LEU* 3.1 20.0 - - + +
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Residues in contact with VAL 94 (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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64A ILE* 3.2 10.8 - - + +
92A LEU* 4.0 13.9 - - + -
93A ALA* 1.3 75.3 - - - +
95A LEU* 1.3 60.2 + - - +
97A ASN* 3.4 18.8 - - - +
115A LEU* 3.8 21.3 - - + -
118A LEU* 3.5 27.4 - - + -
132A LEU 2.7 9.4 + - - +
133A ILE* 3.3 23.5 - - + -
134A GLN 2.9 26.3 + - - -
136A ASN* 3.1 13.6 + - - +
139A LEU* 4.2 7.4 - - + -
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Residues in contact with LEU 95 (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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11A LEU* 4.7 13.2 - - + -
63A LEU* 4.1 11.0 - - + -
64A ILE 2.8 9.7 + - - -
65A ALA* 3.1 11.5 - - + +
66A HIS 3.0 14.0 + - - -
86A PHE* 3.7 30.7 - - + -
87A GLU* 5.3 2.7 - - - +
93A ALA* 4.3 4.7 - - + -
94A VAL* 1.3 86.4 - - - +
96A ASP* 1.3 76.8 + - - +
97A ASN* 2.9 15.2 + - - +
132A LEU* 4.0 22.9 - - + -
134A GLN* 3.4 25.4 - - + -
135A ARG* 4.0 11.2 - - - +
136A ASN* 3.6 0.2 - - - -
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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