Contacts of the helix formed by residues 88 - 96 (chain A) in PDB entry 4HYY
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 ALA 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR* 1.3 72.2 - - - +
89A PHE* 1.3 55.9 + - - +
91A TYR* 4.2 8.3 - - - -
92A SER* 2.9 28.8 + - - -
165B PHE* 3.8 29.4 - - + -
167B PRO* 3.5 6.2 - - - +
170B LEU* 4.8 0.2 - - + -
185B LEU* 3.1 26.9 + - + +
188B VAL* 2.8 26.6 + - + +
190B TYR* 4.8 2.7 - - + +
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Residues in contact with PHE 89 (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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87A THR* 3.0 9.4 - - - +
88A ALA* 1.3 75.1 - - - +
90A GLU* 1.3 75.2 + - + +
92A SER* 3.2 6.4 + - - -
93A GLU* 3.0 51.6 + - + +
182B ASP* 4.0 23.8 - - + -
185B LEU* 3.0 37.1 + - + +
186B ASP* 4.2 16.6 - - - +
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Residues in contact with GLU 90 (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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86A LEU* 3.5 24.7 - - + +
87A THR* 2.7 52.3 + - - +
89A PHE* 1.3 83.6 - - + +
91A TYR* 1.3 63.0 + - - +
93A GLU* 3.1 10.6 + - - +
94A LYS* 3.0 21.0 + - - +
212D GLU 4.5 13.2 - - - +
213D GLU* 5.7 4.7 - - - +
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Residues in contact with TYR 91 (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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86A LEU* 4.0 13.8 - - + +
87A THR 3.0 14.1 + - - +
88A ALA* 3.8 6.5 - - - +
90A GLU* 1.3 72.2 - - - +
92A SER* 1.3 57.7 + - - +
94A LYS* 2.7 37.1 + - + +
95A ARG* 2.8 47.5 + - + +
119A MET* 4.1 21.5 - - + +
258A GLU* 5.0 1.2 + - - -
160B ASP* 5.2 0.2 + - - -
163B ASN* 4.2 7.1 + - - -
165B PHE* 3.5 41.4 + + - -
166B ARG* 4.8 0.2 + - - -
167B PRO* 3.6 13.9 - - + -
190B TYR* 3.5 43.0 + + + -
192B ARG* 5.0 5.0 - - + +
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Residues in contact with SER 92 (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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88A ALA 2.9 19.1 + - - -
89A PHE* 3.2 10.9 + - - -
91A TYR* 1.3 77.1 - - - +
93A GLU* 1.3 63.5 + - - +
95A ARG* 3.2 7.1 + - - +
96A LYS* 3.0 42.6 + - - +
167B PRO* 3.6 22.5 - - - +
168B ASP* 5.1 4.0 + - - -
171B ARG* 5.6 2.8 - - - -
185B LEU* 4.5 10.4 - - - +
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Residues in contact with GLU 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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89A PHE* 3.0 45.1 + - + +
90A GLU* 3.1 12.5 + - + +
92A SER* 1.3 78.6 + - - +
94A LYS* 1.3 63.8 + - - +
96A LYS* 3.4 34.7 + - - +
97A MET* 4.3 10.0 - - - +
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Residues in contact with LYS 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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86A LEU* 4.8 13.5 - - + +
90A GLU 3.0 11.1 + - - +
91A TYR* 2.7 23.9 + - + +
93A GLU* 1.3 81.6 - - - +
95A ARG* 1.3 59.0 + - - +
96A LYS 3.4 0.5 + - - -
97A MET* 3.4 31.3 + - + +
98A VAL 4.3 1.2 + - - -
119A MET* 3.8 25.1 - - + +
258A GLU* 3.3 31.6 + - - +
259A GLU* 4.4 11.9 - - - +
261A ASN* 5.4 2.8 + - - +
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Residues in contact with ARG 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 TYR* 2.8 57.4 + - + +
92A SER* 3.7 9.2 - - - +
94A LYS* 1.3 72.2 - - - +
96A LYS* 1.3 63.7 + - - +
97A MET 2.8 7.3 + - - -
98A VAL* 3.1 47.0 + - + +
117A GLU* 3.8 11.3 + - - -
119A MET* 4.2 22.9 + - - +
163B ASN* 3.9 8.3 + - - -
166B ARG* 3.2 55.3 - - - +
167B PRO* 4.3 9.6 - - + -
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Residues in contact with LYS 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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92A SER* 3.0 33.9 + - - +
93A GLU* 3.8 27.6 - - - +
94A LYS 3.2 1.8 - - - -
95A ARG* 1.3 76.4 - - - +
97A MET* 1.3 61.7 + - + +
98A VAL 3.4 3.6 - - - +
168B ASP* 3.9 19.9 + - - +
171B ARG* 5.0 15.8 - - - +
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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