Contacts of the helix formed by residues 84 - 88 (chain A) in PDB entry 3HCC
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 VAL 84 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A PRO 4.9 0.2 - - - +
83A THR* 1.3 78.6 - - - +
85A TYR* 1.3 70.4 + - - +
86A GLN* 3.0 7.5 + - - -
87A LEU* 3.0 18.8 + - - +
88A LEU* 3.8 7.6 + - + +
99A MET* 4.1 19.1 - - + -
110A LEU* 4.1 11.0 - - + +
113A TRP* 4.0 36.3 - - + -
114A LEU* 5.6 1.1 - - + -
123A TRP* 3.5 41.9 - - + +
147A LEU* 4.0 16.0 - - + +
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A TYR* 2.9 41.4 + + - -
57A LYS* 3.1 35.3 + - + +
58A LEU* 4.0 18.7 - - + +
61A LEU* 4.5 9.1 - - + +
83A THR* 3.5 10.8 - - - -
84A VAL* 1.3 80.3 - - - +
86A GLN* 1.3 83.5 + - + +
87A LEU 2.9 6.3 + - - -
88A LEU* 3.3 31.2 + - + +
89A SER 5.0 0.5 + - - -
123A TRP* 3.9 9.1 - + + -
126A TYR* 3.9 25.6 - + + -
181A ALA* 3.6 6.2 - - + +
182A PHE* 3.4 10.2 - - - -
214A ILE* 5.1 1.3 - - + -
3001A SAH 2.6 25.2 + - - -
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU* 3.9 23.1 - - + +
77A ASP* 2.8 39.9 + - - +
80A SER* 3.4 12.9 + - - +
83A THR* 2.7 45.5 + - - -
84A VAL* 3.0 2.7 + - - -
85A TYR* 1.3 100.7 + - + +
87A LEU* 1.3 66.7 + - + +
88A LEU 3.8 0.2 - - - -
89A SER 5.5 0.4 + - - -
90A ALA* 4.5 4.9 + - - +
99A MET* 4.4 0.6 - - - +
179A VAL* 3.9 16.3 - - + +
181A ALA* 4.4 11.2 - - + -
214A ILE* 5.7 0.9 - - + -
3001A SAH 4.0 6.6 + - - +
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Residues in contact with LEU 87 (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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75A LEU* 4.1 17.3 - - + -
77A ASP* 3.9 28.0 - - + +
84A VAL 3.0 8.6 + - - +
85A TYR 3.0 1.0 - - - -
86A GLN* 1.3 96.6 - - + +
88A LEU* 1.3 60.1 + - - +
89A SER 3.3 2.7 - - - -
90A ALA* 3.6 10.1 - - + -
91A CYS* 2.8 33.3 + - - +
97A ILE* 3.8 18.8 - - + -
99A MET* 3.8 37.2 - - + -
147A LEU* 3.9 18.8 - - + -
151A VAL* 4.9 0.2 - - + -
179A VAL* 4.2 9.6 - - + -
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Residues in contact with LEU 88 (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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58A LEU* 4.5 5.4 - - + -
84A VAL* 3.8 8.2 + - + +
85A TYR* 3.3 33.4 + - + +
86A GLN 3.8 0.2 - - - -
87A LEU* 1.3 77.6 - - - +
89A SER* 1.3 61.6 + - - +
91A CYS* 3.4 9.1 - - - -
113A TRP* 5.4 0.9 - - + -
123A TRP* 5.8 0.9 - - + -
126A TYR* 3.6 37.2 - - + +
127A SER* 3.6 19.7 - - - +
130A ALA* 3.8 16.2 - - + -
134A GLU* 4.1 0.4 - - - -
143A LYS* 3.1 44.0 + - + +
144A GLU* 5.2 3.6 - - + -
147A LEU* 4.2 18.6 - - + -
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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