Contacts of the helix formed by residues 86 - 92 (chain B) in PDB entry 4KYI
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 LEU 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A PHE* 3.7 33.0 - - + -
443A GLU* 3.7 29.8 - - + +
446A ALA* 3.6 22.2 - - + -
447A HIS* 3.5 32.1 - - + +
83B TYR* 3.2 23.5 + - + +
84B HIS 3.2 1.0 - - - -
85B SER* 1.3 81.0 - - - +
87B ALA* 1.3 62.9 + - - +
88B PRO* 3.6 1.6 - - - -
89B MET* 3.5 15.6 + - + +
90B TYR* 3.1 29.3 - - + +
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Residues in contact with ALA 87 (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 LEU* 5.0 6.1 - - + -
77B THR* 6.3 0.2 - - - -
83B TYR 3.6 4.4 + - - +
84B HIS 3.3 16.3 + - - +
85B SER 3.3 0.2 - - - -
86B LEU* 1.3 73.3 - - - +
88B PRO* 1.4 65.5 - - + +
89B MET 3.1 2.5 - - - -
90B TYR* 2.8 29.5 + - - +
91B TYR* 3.3 28.5 + - + -
115B TRP* 3.9 24.2 - - + -
118B GLU* 4.8 2.7 - - - +
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Residues in contact with PRO 88 (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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484A ASP* 4.5 4.7 - - - +
84B HIS 4.2 1.8 - - - +
85B SER* 3.7 14.4 - - - +
86B LEU 3.7 2.7 - - - -
87B ALA* 1.4 93.8 - - + +
89B MET* 1.3 59.8 + - - +
91B TYR* 3.8 30.2 - - + +
92B ARG* 3.1 33.2 + - + +
118B GLU* 5.4 2.9 - - - +
122B GLN* 5.7 5.4 - - + -
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Residues in contact with MET 89 (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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446A ALA* 3.8 18.4 - - + +
447A HIS* 3.5 32.3 - - + +
450A ALA* 4.2 3.1 - - + -
480A ILE* 3.8 24.9 - - + -
484A ASP* 3.3 30.0 + - + +
23B LYS* 3.7 4.7 + - - -
86B LEU* 3.5 13.1 + - + +
87B ALA 3.0 0.6 + - - -
88B PRO* 1.3 79.6 - - - +
90B TYR* 1.3 92.0 + - + +
91B TYR 3.9 0.2 + - - -
92B ARG* 3.7 8.8 + - - +
303B EDO 2.3 40.4 + - - +
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Residues in contact with TYR 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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446A ALA* 4.3 14.6 + - - +
449A GLN* 4.4 2.6 + - - +
450A ALA* 4.9 0.6 - - + +
23B LYS* 3.2 21.6 - - - -
25B VAL* 3.9 20.6 - - + +
27B LEU* 5.7 0.7 - - + -
55B GLY* 4.1 11.6 - - - -
56B ALA* 3.4 24.8 + - + +
75B TRP* 3.4 45.9 - + + +
77B THR* 3.9 26.0 - - + -
83B TYR* 5.5 3.4 - + + -
86B LEU* 3.1 38.0 - - + +
87B ALA* 2.8 11.6 + - - +
89B MET* 1.3 103.5 - - + +
91B TYR* 1.3 56.7 + - + +
92B ARG 3.6 0.7 - - - -
303B EDO 3.7 6.5 - - - -
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Residues in contact with TYR 91 (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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25B VAL* 4.0 17.0 - - + -
27B LEU* 4.5 10.5 - - + -
87B ALA* 3.3 38.6 + - + -
88B PRO* 3.8 25.3 - - + +
90B TYR* 1.3 77.4 - - + +
92B ARG* 1.3 67.4 + - - +
93B GLY 3.3 3.1 - - - -
94B ALA* 3.5 19.4 + - + +
115B TRP* 5.1 3.4 - + - -
118B GLU* 3.8 24.7 + - + +
119B LEU* 4.0 24.0 - - + -
122B GLN* 3.4 25.4 - - + +
123B ALA* 3.7 41.1 - - + +
124B SER 4.7 1.0 + - - -
127B ILE* 5.3 0.4 - - + -
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Residues in contact with ARG 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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476A GLN* 6.1 0.2 - - - +
479A ASP* 2.4 49.2 + - - +
480A ILE* 4.4 3.0 - - - +
483A VAL* 3.7 23.6 - - - +
484A ASP* 2.3 41.2 + - - -
23B LYS* 5.4 0.8 - - - +
88B PRO* 3.1 20.2 + - + +
89B MET* 3.7 17.6 + - - +
90B TYR 3.6 1.8 - - - -
91B TYR* 1.3 82.3 - - + +
93B GLY* 1.3 59.0 + - - +
123B ALA* 6.0 0.7 - - - +
124B SER* 5.0 11.3 + - - -
303B EDO 5.1 8.1 - - - -
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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