Contacts of the helix formed by residues 77 - 87 (chain B) in PDB entry 5L9Y
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 SER 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A PHE* 3.8 24.3 - - - -
73B ILE 3.2 6.7 + - - -
74B LEU 3.2 18.0 + - - -
75B LEU 3.3 0.4 - - - -
76B GLY* 1.3 73.4 - - - +
78B PRO* 1.4 69.3 - - - +
79B LYS* 3.3 12.1 + - - +
80B LEU* 3.1 23.7 + - - +
81B ARG* 3.0 24.1 + - - +
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Residues in contact with PRO 78 (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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505A ASP* 5.4 4.0 - - + +
506A GLN* 3.5 22.2 + - - +
76B GLY 3.2 9.6 - - - +
77B SER* 1.4 82.2 - - - +
79B LYS* 1.3 57.5 + - - +
81B ARG* 3.3 10.6 + - + +
82B THR* 2.9 31.2 + - - -
85B ARG* 4.2 0.8 + - - +
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Residues in contact with LYS 79 (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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397A ASN 3.5 9.9 + - - +
398A PHE* 3.3 33.4 - - + +
399A ASP* 2.8 26.3 + - - +
502A MET* 3.9 25.7 - - + +
505A ASP* 3.5 43.5 + - - +
77B SER* 3.2 8.6 + - - +
78B PRO* 1.3 75.8 - - - +
80B LEU* 1.3 67.0 + - - +
82B THR* 3.2 4.3 + - - -
83B LEU* 3.1 23.0 + - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE* 4.1 16.8 - - + -
385A PHE* 3.5 27.8 - - + -
386A PHE* 3.8 27.6 - - + -
394A VAL* 3.7 27.8 - - + -
398A PHE* 3.8 13.2 - - + +
74B LEU 3.5 19.1 - - - +
75B LEU* 4.1 11.0 - - + -
77B SER* 3.1 21.4 + - - +
79B LYS* 1.3 76.7 - - - +
81B ARG* 1.3 58.8 + - - +
83B LEU* 3.2 6.1 + - + +
84B ALA* 2.9 29.0 + - - +
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Residues in contact with ARG 81 (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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172A VAL* 4.8 2.8 + - - +
175A THR* 3.6 25.0 - - - +
176A PHE* 3.9 29.6 - - + +
179A CYS* 3.7 27.7 - - - +
180A SER* 3.7 10.7 + - - +
75B LEU 3.0 23.0 + - - -
76B GLY* 3.9 18.7 + - - -
77B SER 3.0 17.8 + - - +
78B PRO* 3.6 11.0 - - + +
79B LYS 3.3 0.2 - - - -
80B LEU* 1.3 76.8 - - - +
82B THR* 1.3 55.3 + - - +
84B ALA* 3.3 2.5 + - - +
85B ARG* 2.9 55.6 + - - +
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Residues in contact with THR 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A MET* 3.7 20.2 - - + -
505A ASP 2.9 20.1 + - - -
506A GLN* 3.4 37.8 + - - +
507A THR 4.0 0.7 - - - +
508A LEU* 4.1 15.8 - - + +
78B PRO 2.9 11.0 + - - -
79B LYS 3.2 5.6 + - - -
81B ARG* 1.3 76.6 - - - +
83B LEU* 1.3 61.9 + - - +
85B ARG* 3.3 19.8 + - - +
86B GLY* 3.2 18.5 + - - -
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Residues in contact with LEU 83 (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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385A PHE* 4.1 8.3 - - + -
394A VAL* 3.9 20.9 - - + -
398A PHE 3.3 26.9 - - - +
400A PRO* 3.9 20.9 - - + -
404A TYR* 2.6 59.7 + - + +
502A MET* 3.8 22.0 - - + -
508A LEU* 4.1 7.6 - - + -
79B LYS 3.1 15.5 + - - +
80B LEU* 3.6 7.4 - - - +
82B THR* 1.3 75.3 - - - +
84B ALA* 1.3 63.0 + - - +
86B GLY* 3.2 6.6 + - - -
87B LEU* 3.7 2.8 + - - +
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Residues in contact with ALA 84 (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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176A PHE* 3.8 17.7 - - + -
180A SER* 3.4 31.2 - - - +
182A LEU* 3.9 14.3 - - + +
385A PHE* 3.6 14.6 - - + -
80B LEU 2.9 16.6 + - - +
81B ARG 3.5 0.7 - - - +
83B LEU* 1.3 77.4 - - - +
85B ARG* 1.3 61.2 + - - +
87B LEU* 3.1 17.1 + - - +
88B SER 3.6 5.9 + - - -
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A CYS* 3.1 27.7 + - - +
180A SER* 3.4 24.2 + - - +
412A LYS* 5.4 0.2 + - - -
506A GLN* 3.8 19.2 + - - +
78B PRO* 4.2 0.8 + - - +
81B ARG* 2.9 37.9 + - - +
82B THR* 3.3 36.7 + - - +
84B ALA* 1.3 72.7 - - - +
86B GLY* 1.3 61.5 + - - +
88B SER* 3.1 20.9 + - - +
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Residues in contact with GLY 86 (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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404A TYR* 3.9 1.6 - - - -
408A LEU* 3.3 13.7 - - - +
411A LYS* 4.6 0.9 - - - +
412A LYS* 2.9 29.7 + - - -
508A LEU* 3.7 24.2 - - - +
82B THR 3.2 10.9 + - - -
83B LEU 3.2 6.5 + - - -
84B ALA 3.2 1.0 - - - -
85B ARG* 1.3 76.9 - - - +
87B LEU* 1.3 58.4 + - - +
88B SER 3.7 0.3 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A LEU* 4.6 1.6 - - + -
385A PHE* 4.0 23.6 - - + -
393A LEU* 4.2 15.0 - - + -
404A TYR* 3.9 29.8 - - + -
407A SER* 4.3 8.3 - - - -
408A LEU* 4.1 24.5 - - + +
411A LYS* 2.9 45.7 + - + +
57B LEU* 5.3 4.0 - - + +
59B VAL* 4.2 13.2 - - + -
83B LEU 3.9 2.5 - - - +
84B ALA* 3.1 10.0 + - - +
86B GLY* 1.3 77.5 - - - +
88B SER* 1.3 62.6 + - - +
89B PRO 3.3 4.0 - - - +
90B ALA* 3.5 10.1 - - + +
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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