Contacts of the strand formed by residues 91 - 97 (chain B) in PDB entry 1HJV
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 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52B THR 3.1 10.0 + - - +
53B HIS* 3.3 32.7 - - + +
54B ILE 3.0 22.7 + - - -
88B PRO 5.7 2.3 + - - -
89B ASN* 3.7 16.4 - - - +
90B LEU* 1.3 82.7 - - - +
92B THR* 1.3 65.4 + - - +
93B LEU* 4.7 0.2 - - - -
133B ASP* 3.0 33.3 + - + +
170B LYS* 4.0 33.5 - - - +
173B LEU* 4.3 14.4 - - + -
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Residues in contact with THR 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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54B ILE* 3.2 11.4 - - + +
80B LEU* 4.0 24.2 - - + +
81B ASN* 3.0 23.4 + - - +
84B LYS* 3.2 32.2 + - + -
90B LEU* 4.6 9.2 - - + -
91B LYS* 1.3 77.9 - - - +
93B LEU* 1.3 67.2 + - - +
132B PHE* 3.4 12.7 - - - -
133B ASP* 2.6 38.5 + - - +
134B GLY 3.4 1.4 + - - -
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Residues in contact with LEU 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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53B HIS* 4.0 31.2 - - + -
54B ILE 3.1 5.9 + - - -
55B ILE* 4.1 24.2 - - + -
56B TYR* 2.8 30.0 + - - +
92B THR* 1.3 85.2 - - - +
94B LEU* 1.3 60.2 + - - +
95B SER 3.9 0.2 - - - -
132B PHE* 3.8 7.8 - - - -
134B GLY* 3.2 18.6 - - - +
135B LEU 3.4 24.5 - - - +
136B ASP* 4.3 3.6 - - + -
173B LEU* 4.3 17.5 - - + -
175B SER* 3.7 21.1 - - - +
200B PHE* 4.2 8.1 - - + -
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Residues in contact with LEU 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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56B TYR* 3.7 33.2 - - + +
59B ALA* 3.6 31.9 - - + +
66B ILE* 4.0 12.3 - - + -
77B TYR* 3.8 14.4 - - + +
93B LEU* 1.3 73.4 - - - +
95B SER* 1.3 54.9 + - - +
126B PHE* 3.6 32.3 - - + -
127B LEU* 4.2 11.0 - - + -
132B PHE* 4.0 22.1 - - + -
134B GLY 3.0 7.1 + - - -
135B LEU* 2.6 34.2 - - + +
136B ASP* 3.0 7.3 + - - -
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Residues in contact with SER 95 (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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27B TYR* 3.8 1.8 - - - -
55B ILE* 3.3 19.6 - - - +
56B TYR 2.7 18.6 + - - -
57B SER* 3.6 12.3 - - - -
58B PHE* 3.0 26.9 - - - -
59B ALA* 2.8 26.0 + - - +
94B LEU* 1.3 70.9 - - - +
96B VAL* 1.3 58.6 + - - +
136B ASP* 2.9 23.4 + - - -
138B ALA* 3.7 3.6 - - - +
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Residues in contact with VAL 96 (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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59B ALA* 3.3 23.3 - - + +
60B ASN 4.0 4.5 - - - +
61B ILE* 3.6 32.5 - - + -
66B ILE* 4.8 3.8 - - + -
94B LEU 3.5 0.6 + - - -
95B SER* 1.3 74.3 - - - +
97B GLY* 1.3 59.5 + - - +
98B GLY 4.2 0.4 - - - -
101B PHE* 4.8 0.2 - - + -
106B PHE* 3.6 5.3 - - + -
119B PHE* 4.2 9.9 - - + -
135B LEU* 3.9 21.3 - - + -
136B ASP 2.7 17.2 + - - +
137B LEU* 3.6 24.5 - - + -
138B ALA* 2.8 22.9 + - - -
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Residues in contact with GLY 97 (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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58B PHE* 3.7 16.6 - - - +
59B ALA 3.6 5.1 + - - -
69B TRP* 4.3 4.3 - - - -
96B VAL* 1.3 79.3 - - - +
98B GLY* 1.3 64.0 + - - -
101B PHE* 3.1 27.7 + - - +
106B PHE* 3.5 15.5 - - - -
138B ALA 3.0 8.3 - - - -
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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