Contacts of the helix formed by residues 92 - 101 (chain D) in PDB entry 3K75
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 92 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D ASP* 1.3 80.8 - - - +
93D THR* 1.3 61.1 + - - +
94D SER* 4.3 4.7 - - - +
95D SER* 2.8 40.8 + - - +
96D SER* 3.0 12.5 + - - -
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Residues in contact with THR 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ASP 3.6 3.2 + - - -
92D ASP* 1.3 73.4 - - - +
94D SER* 1.3 60.9 + - - +
96D SER* 3.1 8.6 + - - -
97D ILE* 2.9 43.1 + - + +
112D ARG* 5.9 7.0 - - + +
115D VAL* 4.3 19.2 - - + +
120D LYS* 5.7 5.4 - - - +
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Residues in contact with SER 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D ASP* 3.2 4.1 - - - +
93D THR* 1.3 77.8 - - - +
95D SER* 1.3 57.0 + - - +
97D ILE* 4.0 8.5 - - - -
98D ASN* 2.6 51.7 + - - -
112D ARG* 5.8 4.0 + - - +
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Residues in contact with SER 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ASP* 4.9 6.5 - - - -
92D ASP* 2.8 36.4 + - - +
94D SER* 1.3 83.0 - - - +
96D SER* 1.3 59.4 + - - +
98D ASN* 3.4 12.4 + - - +
99D PHE* 3.3 18.9 + - - +
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Residues in contact with SER 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D ASP* 5.4 3.5 + - - +
92D ASP 3.0 10.4 + - - -
93D THR* 3.1 11.0 + - - -
95D SER* 1.3 75.6 - - - +
97D ILE* 1.3 64.7 + - - +
99D PHE* 3.4 8.2 + - - +
100D LEU* 3.3 25.6 + - - +
115D VAL* 4.6 6.5 - - - -
120D LYS* 3.0 50.8 + - - +
121D THR* 5.6 0.2 - - - +
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Residues in contact with ILE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 2.9 26.0 + - + +
94D SER* 3.5 9.0 - - - +
96D SER* 1.3 74.0 - - - +
98D ASN* 1.3 72.0 + - - +
99D PHE 2.9 3.2 + - - -
100D LEU* 3.0 16.0 + - - +
101D THR* 3.3 14.8 + - - +
108D PRO* 5.0 5.6 - - + +
111D ALA* 3.5 25.4 - - + +
112D ARG* 3.6 39.7 - - + +
115D VAL* 3.2 26.7 - - + -
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Residues in contact with ASN 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94D SER* 2.6 47.8 + - - +
95D SER* 3.5 11.1 + - - +
96D SER 3.4 0.2 - - - -
97D ILE* 1.3 78.5 - - - +
99D PHE* 1.3 61.8 + - - +
101D THR* 3.7 12.9 + - - +
102D ARG* 3.5 16.4 - - - +
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Residues in contact with PHE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D SER 3.3 9.8 + - - +
96D SER* 3.4 11.7 - - - +
97D ILE 2.9 0.8 + - - -
98D ASN* 1.3 77.5 - - - +
100D LEU* 1.3 76.9 + - + +
102D ARG* 3.0 37.0 + - - +
103D VAL* 4.1 8.1 + - + +
120D LYS 4.0 12.8 - - - +
121D THR* 4.1 4.0 - - - -
122D LEU* 3.5 46.7 - - + -
143D PHE* 4.6 19.9 - + - -
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Residues in contact with LEU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D SER 3.3 15.7 + - - +
97D ILE* 3.0 7.1 + - - +
99D PHE* 1.3 84.4 - - + +
101D THR* 1.3 62.6 + - - +
103D VAL* 3.0 24.7 + - - +
106D ILE* 3.5 20.5 - - + +
111D ALA* 3.6 25.1 - - + +
114D LEU* 4.1 8.5 - - + -
115D VAL* 3.9 8.1 - - + -
119D ILE 3.3 26.0 - - - +
120D LYS* 3.9 13.2 - - - +
121D THR 4.5 0.7 - - - +
125D LEU* 3.3 39.7 - - + -
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Residues in contact with THR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.3 11.8 + - - +
98D ASN* 3.8 13.8 - - - +
99D PHE 3.2 0.6 - - - -
100D LEU* 1.3 79.0 - - - +
102D ARG* 1.3 59.2 + - + +
103D VAL 2.9 15.1 - - - +
106D ILE* 3.3 20.7 + - - +
107D GLY* 5.5 2.2 - - - -
108D PRO* 4.4 14.1 - - + +
111D ALA* 4.2 9.0 - - - +
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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