Contacts of the helix formed by residues 85 - 95 (chain L) in PDB entry 5XVO
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 ASP 85 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208K PHE* 4.7 17.8 + - - +
210K ASP* 5.3 0.9 - - - -
83L ARG* 3.4 19.1 + - - +
84L HIS* 1.3 118.5 + - - +
86L SER* 1.3 65.7 + - - +
87L SER* 2.9 7.7 + - - +
88L LEU* 3.1 23.2 + - + +
89L GLN 4.2 0.5 + - - -
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Residues in contact with SER 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199K GLN* 2.9 28.7 + - - -
210K ASP* 4.1 10.5 + - - -
80L PHE 4.8 0.9 + - - -
81L TYR* 5.0 2.5 - - - -
82L GLY 4.7 6.3 + - - -
83L ARG* 3.6 34.2 + - - +
84L HIS 4.0 0.4 + - - -
85L ASP* 1.3 74.6 - - - +
87L SER* 1.3 63.7 + - - +
88L LEU 3.3 0.9 + - - -
89L GLN* 3.3 10.2 + - - +
90L LEU* 3.3 12.0 + - - +
195L GLY* 3.8 21.1 + - - +
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Residues in contact with SER 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199K GLN* 4.2 7.7 + - - +
200K LEU* 4.2 17.8 - - - +
208K PHE 4.5 13.3 + - - -
209K ASN 3.5 23.0 + - - -
210K ASP* 4.4 4.0 + - - -
212K ASN* 5.7 1.6 - - - -
85L ASP* 2.9 4.4 + - - -
86L SER* 1.3 78.9 + - - +
88L LEU* 1.3 63.8 + - - +
89L GLN 3.2 0.3 + - - -
90L LEU* 3.2 20.1 + - - +
91L THR* 3.2 18.5 + - - -
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Residues in contact with LEU 88 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L ARG* 5.6 11.9 - - - +
85L ASP* 3.1 18.3 + - + +
87L SER* 1.3 80.9 - - - +
89L GLN* 1.3 62.6 + - - +
91L THR* 3.7 8.1 + - - +
92L ARG* 3.2 58.4 + - + +
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Residues in contact with GLN 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L ARG* 4.4 12.8 + - - +
85L ASP 4.2 1.0 + - - +
86L SER 3.3 6.0 + - - +
87L SER 3.2 0.6 - - - -
88L LEU* 1.3 80.8 - - - +
90L LEU* 1.3 59.8 + - - +
92L ARG* 3.1 10.2 + - - +
93L GLN* 2.8 28.3 + - - +
96L TRP* 3.9 6.3 - - - -
194L THR 3.4 26.3 - - - +
195L GLY* 3.6 17.9 - - - +
196L CYS* 3.7 15.6 - - - -
273L VAL* 3.6 18.3 - - - +
277L ASN* 3.1 41.2 + - - +
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Residues in contact with LEU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197K PHE* 4.7 4.9 - - + -
199K GLN* 3.1 46.4 - - + +
200K LEU* 4.2 17.7 - - + -
86L SER* 3.3 9.5 + - - +
87L SER* 3.2 11.1 + - - +
89L GLN* 1.3 78.8 - - - +
91L THR* 1.3 64.5 + - - +
93L GLN* 3.1 9.8 + - + +
94L LEU* 3.0 32.5 + - + +
195L GLY 3.8 13.6 + - - +
197L PHE* 3.1 46.4 - - + -
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Residues in contact with THR 91 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200K LEU* 4.3 14.5 - - + +
87L SER 3.2 12.7 + - - -
88L LEU* 3.9 9.3 + - - +
89L GLN 3.3 0.4 - - - -
90L LEU* 1.3 77.2 - - - +
92L ARG* 1.3 63.0 + - - +
94L LEU* 3.3 13.6 + - + +
95L ALA* 3.2 21.4 + - + +
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Residues in contact with ARG 92 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88L LEU* 3.2 52.1 + - + +
89L GLN* 3.1 15.8 + - - +
91L THR* 1.3 81.8 - - - +
93L GLN* 1.3 61.7 + - - +
95L ALA* 3.1 17.4 + - - +
96L TRP* 3.2 17.9 + - - -
277L ASN* 3.6 27.5 - - + +
279L GLU* 3.3 29.1 + - - +
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Residues in contact with GLN 93 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89L GLN* 2.8 19.0 + - - +
90L LEU* 3.5 10.8 - - + +
92L ARG* 1.3 74.5 - - - +
94L LEU* 1.3 64.4 + - + +
96L TRP* 3.2 51.0 + - + +
195L GLY 4.4 1.4 - - - +
196L CYS* 3.1 13.5 - - - -
197L PHE* 2.8 51.1 + - - +
200L LEU* 3.7 29.3 - - + +
213L LEU* 3.8 12.7 - - - +
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Residues in contact with LEU 94 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K LEU* 3.5 36.8 - - + -
197K PHE* 5.3 1.3 - - + -
200K LEU* 4.2 22.9 - - + -
90L LEU* 3.0 26.2 + - + +
91L THR* 3.6 10.1 - - + +
92L ARG 3.3 0.2 - - - -
93L GLN* 1.3 77.5 - - + +
95L ALA* 1.3 59.0 + - - +
96L TRP 3.6 3.6 + - - +
197L PHE* 5.5 0.2 - - + -
200L LEU* 4.2 19.5 - - + -
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Residues in contact with ALA 95 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91L THR* 3.2 11.5 + - + +
92L ARG* 3.1 13.6 + - - +
93L GLN 3.1 0.6 - - - -
94L LEU* 1.3 76.4 - - - +
96L TRP* 1.3 65.2 + - - +
97L THR* 3.1 12.0 + - - +
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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