Contacts of the helix formed by residues 86 - 93 (chain L) in PDB entry 1FQV
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 PRO 86 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64L HIS* 6.0 1.6 - - - +
65L HIS* 5.0 6.1 - - - +
85L ILE* 1.3 102.1 - - + +
87L VAL* 1.3 61.1 + - - +
88L TRP* 4.4 3.8 - - + +
89L ASP* 3.7 29.6 - - - +
90L GLN* 2.9 23.2 + - - +
118L VAL* 4.8 4.9 - - + -
245O VAL* 6.4 1.6 - - + -
269O ARG 6.0 1.8 - - - +
271O ASP* 4.8 11.4 - - + +
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Residues in contact with VAL 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85L ILE 3.6 0.4 + - - +
86L PRO* 1.3 69.8 - - - +
88L TRP* 1.3 63.3 + - - +
90L GLN* 2.9 17.0 + - + +
91L GLU* 2.8 32.3 + - + +
271O ASP* 4.8 2.0 + - - -
295O GLU* 4.2 1.1 - - + +
296O THR* 3.1 46.3 + - + +
298O THR* 3.6 10.8 - - + -
323O ASN* 3.3 47.1 - - + +
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Residues in contact with TRP 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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60L GLN* 3.7 27.5 + - + -
61L TRP* 3.9 30.1 - + - -
64L HIS* 3.5 58.3 + + + +
86L PRO* 3.4 3.1 - - + +
87L VAL* 1.3 80.1 - - - +
89L ASP* 1.3 84.1 + - - +
91L GLU* 2.7 46.4 + - + +
92L PHE* 2.8 33.6 + + - +
269O ARG* 6.1 2.2 - - + -
296O THR* 4.6 13.6 - - + +
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Residues in contact with ASP 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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61L TRP* 3.3 23.9 + - - +
64L HIS* 4.1 1.7 - - - -
65L HIS* 3.1 21.4 + - - -
85L ILE* 3.5 21.3 - - + -
86L PRO* 3.4 20.5 + - + +
87L VAL 3.1 0.4 - - - -
88L TRP* 1.3 90.5 - - - +
90L GLN* 1.3 62.3 + - - +
92L PHE* 3.2 7.5 - - - +
93L LEU* 2.8 34.7 + - + +
118L VAL* 3.5 19.9 - - + +
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Residues in contact with GLN 90 (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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85L ILE* 3.0 34.6 + - + +
86L PRO 2.9 21.6 + - - +
87L VAL* 2.9 18.5 + - + +
89L ASP* 1.3 74.2 - - - +
91L GLU* 1.3 65.4 + - - +
93L LEU* 3.2 6.0 + - - -
94L LYS* 3.1 23.8 + - - +
323O ASN* 5.1 6.3 + - - +
348O TYR* 6.1 5.5 - - - -
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Residues in contact with GLU 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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60L GLN* 5.4 1.2 - - - +
87L VAL* 2.8 13.2 + - + +
88L TRP* 2.7 57.0 + - + +
90L GLN* 1.3 74.8 - - - +
92L PHE* 1.3 83.7 + - - +
94L LYS* 3.0 25.4 + - - +
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Residues in contact with PHE 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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57L LYS* 3.1 87.8 + - + +
58L VAL* 5.2 0.2 - - - -
60L GLN* 3.6 17.3 - - - -
61L TRP* 3.6 30.1 - + + -
88L TRP* 2.8 39.2 + + + +
89L ASP* 3.2 8.3 - - - +
91L GLU* 1.3 94.2 + - - +
93L LEU* 1.3 90.5 + - + +
94L LYS 3.3 3.3 + - - -
95L VAL* 3.7 8.0 - - - +
103L LEU* 4.4 4.3 - - + -
115L LEU* 4.1 6.1 - - + -
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Residues in contact with LEU 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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85L ILE* 5.5 1.6 - - + -
89L ASP* 2.8 25.4 + - + +
90L GLN* 3.5 7.0 - - - +
91L GLU 3.2 0.2 - - - -
92L PHE* 1.3 102.7 - - + +
94L LYS* 1.3 55.9 + - - +
95L VAL* 3.1 21.0 + - + +
100L LEU* 4.4 8.2 - - + +
103L LEU* 3.7 21.5 - - + -
115L LEU* 5.0 0.2 - - + -
118L VAL* 4.0 26.7 - - + +
119L THR* 4.1 14.6 - - + +
122L THR* 3.1 43.0 - - + +
126L MET* 5.4 3.5 - - - +
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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