Contacts of the helix formed by residues 92 - 99 (chain A) in PDB entry 6D1U
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 TYR 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A LEU* 1.3 71.9 - - - +
93A PRO* 1.4 74.3 - - + +
94A PHE* 3.6 31.0 - + + -
95A THR* 2.6 31.2 + - + -
96A TRP* 3.5 4.0 + - - -
112A VAL* 6.5 0.2 - - + -
304A VAL 3.8 7.2 - - - -
305A ALA* 3.0 26.8 + - - -
307A LYS* 3.8 36.7 + - + +
310A GLU* 2.7 51.1 + - + +
311A GLU* 4.4 7.6 + - - +
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Residues in contact with PRO 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU 3.4 4.7 - - - +
92A TYR* 1.4 90.7 - - + +
94A PHE* 1.3 63.2 + - + +
96A TRP* 3.1 24.7 + - + +
97A ASP* 3.1 20.2 + - - +
307A LYS* 4.6 9.0 - - - +
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Residues in contact with PHE 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A TYR* 3.6 33.0 - + + -
93A PRO* 1.3 78.9 - - + +
95A THR* 1.3 66.0 + - + +
97A ASP* 3.5 18.1 + - + +
98A ALA* 3.4 20.1 + - - +
112A VAL* 3.7 38.6 - - + -
261A VAL* 6.0 1.6 - - + -
263A VAL* 5.3 3.1 - - + -
323A MET* 6.0 4.5 - - - -
331A ILE* 4.8 13.0 - - + +
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Residues in contact with THR 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.8 3.1 - - - +
92A TYR* 2.6 30.7 + - + +
94A PHE* 1.3 86.8 - - + +
96A TRP* 1.3 65.1 + - - +
98A ALA* 3.4 18.3 + - - +
99A VAL* 3.7 3.6 + - - +
109A PRO* 3.5 38.2 - - - +
112A VAL* 4.0 25.1 - - + -
263A VAL* 4.5 6.5 - - + -
305A ALA* 3.6 25.2 - - + +
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Residues in contact with TRP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ILE* 3.9 21.3 - - + -
83A PRO* 3.9 15.0 - - + -
87A PHE* 4.0 16.4 - + - -
88A GLN* 2.9 54.5 + - + +
91A LEU* 3.6 27.7 - - + +
92A TYR 3.9 12.8 - - - -
93A PRO* 3.1 13.9 + - + +
95A THR* 1.3 76.1 + - - +
97A ASP* 1.3 64.1 + - - +
99A VAL* 3.1 24.6 + - + +
100A ARG* 3.3 22.3 + - - +
105A LEU* 3.8 24.4 - - + +
107A ALA 4.1 0.2 - - - -
108A TYR* 4.2 5.2 - + - -
109A PRO* 3.4 26.7 - - + -
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Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A PRO* 3.1 18.7 + - - +
94A PHE* 3.6 18.3 - - + +
95A THR 3.3 0.4 - - - -
96A TRP* 1.3 75.4 - - - +
98A ALA* 1.3 61.9 + - - +
100A ARG* 3.0 43.3 + - - +
331A ILE* 6.4 0.4 - - + -
334A ASN* 5.1 0.3 + - - -
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 3.3 32.7 - - + +
94A PHE 3.4 4.7 + - - +
95A THR 3.6 11.2 - - - +
96A TRP 3.2 0.4 - - - -
97A ASP* 1.3 80.9 - - - +
99A VAL* 1.3 57.4 + - + +
100A ARG 3.4 0.7 - - - -
263A VAL* 3.8 19.7 - - + -
331A ILE* 3.7 28.9 - - + +
334A ASN* 3.6 13.2 + - - -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A HIS* 4.4 4.9 - - + -
69A PHE* 6.1 1.8 - - + -
95A THR 3.7 12.8 - - - +
96A TRP* 3.2 28.5 - - + +
98A ALA* 1.3 79.9 - - + +
100A ARG* 1.3 58.9 + - - +
105A LEU* 3.5 4.4 - - + -
106A ILE* 2.9 35.7 + - - +
107A ALA* 3.2 37.5 - - + +
109A PRO* 4.1 7.9 - - + -
265A SER* 3.3 34.1 - - - +
334A ASN* 4.6 0.7 - - - +
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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