Contacts of the helix formed by residues 95 - 99 (chain A) in PDB entry 3M8D
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 95 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.2 31.6 - - + +
64A SER 3.1 18.5 + - - -
85A LEU* 5.1 4.5 - - - +
93A SER 3.6 0.6 + - - -
94A ALA* 1.3 73.1 - - - +
96A LEU* 1.3 57.4 + - - +
97A SER* 2.4 36.2 + - - -
98A GLN* 3.1 18.3 + - + +
99A PHE 4.4 0.9 + - - -
243A ARG* 2.8 32.5 + - - +
701A CNC 3.9 9.2 - - + +
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Residues in contact with LEU 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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42A VAL* 4.2 20.3 + - + +
43A ASN* 3.8 17.8 + - - +
46A LEU* 3.6 25.6 - - + -
54A ILE* 5.7 0.2 - - + -
64A SER* 3.9 5.1 + - - +
66A ILE* 3.2 40.6 - - + +
78A VAL* 4.2 27.4 - - + -
85A LEU* 4.3 13.7 - - + -
94A ALA* 3.7 4.4 + - + -
95A ASP* 1.3 66.4 + - - +
97A SER* 1.3 65.4 + - - +
98A GLN 2.8 3.7 + - - -
99A PHE* 3.3 26.2 + - + +
127A VAL* 5.8 0.7 - - + -
129A ILE* 4.4 15.3 - - + -
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Residues in contact with SER 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A SER* 5.4 7.8 - - - -
43A ASN* 3.6 13.0 - - - +
56A GLN* 4.1 2.7 - - - -
61A GLY* 3.9 13.2 + - - +
62A GLN 3.1 28.0 + - - -
64A SER* 3.2 9.4 + - - -
95A ASP* 2.4 32.6 + - - -
96A LEU* 1.3 77.8 - - - +
98A GLN* 1.3 68.3 + - - +
99A PHE 4.4 2.8 - - - +
197A PHE* 4.0 17.3 - - - -
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Residues in contact with GLN 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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61A GLY* 3.0 28.9 + - - -
95A ASP* 3.6 20.9 - - + +
96A LEU 2.8 1.0 + - - -
97A SER* 1.3 90.6 + - - +
99A PHE* 1.3 64.2 + - - +
100A PRO* 3.4 8.3 - - - +
197A PHE* 4.0 5.5 - - - -
199A SER* 5.0 0.5 + - - -
223A TYR* 3.6 7.2 - - + +
225A ASN* 2.8 56.2 + - - +
227A THR* 3.3 12.3 + - - -
243A ARG* 3.5 21.7 + - - +
245A LEU* 3.5 25.0 - - + +
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Residues in contact with PHE 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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41A SER* 5.5 1.0 - - - -
42A VAL* 3.6 21.0 + - + +
80A ILE* 3.5 42.6 - - + -
85A LEU* 4.5 9.0 - - + -
95A ASP 4.4 0.6 + - - -
96A LEU* 3.3 24.3 + - + +
97A SER 4.4 2.8 - - - +
98A GLN* 1.3 77.9 - - - +
100A PRO* 1.3 85.1 - - + +
101A ILE 3.3 2.6 + - - -
103A LEU* 4.1 21.3 - - + -
104A VAL* 4.0 22.2 - - + -
129A ILE* 4.0 14.1 - - + -
131A THR* 4.6 3.4 - - + -
221A TYR* 3.8 20.4 - + - -
223A TYR* 3.8 21.3 + + - +
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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