Contacts of the helix formed by residues 95 - 106 (chain B) in PDB entry 4QKH
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 ASN 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B LYS* 1.3 73.9 - - - +
96B TRP* 1.3 63.4 + - - +
97B THR* 3.2 5.9 + - - -
98B SER* 2.8 26.4 + - - -
99B SER* 2.8 26.2 + - - -
132B TRP* 3.5 1.1 - - - -
176B CYS 3.4 9.9 - - - +
177B TYR* 3.6 12.2 + - - +
178B THR 3.0 17.7 - - - +
179B GLU* 4.1 5.9 - - + +
301B NAG 1.5 60.0 + - - +
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Residues in contact with TRP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 1.3 71.9 - - - +
97B THR* 1.3 74.4 + - + +
99B SER* 3.3 4.2 + - - -
100B GLN* 3.0 32.2 + - + -
110B LEU* 3.6 15.2 - - + +
132B TRP* 3.5 42.5 - + + +
133B ILE 2.9 21.2 + - - -
135B LEU 3.7 17.7 + - - -
136B SER* 3.9 28.3 - - - -
146B ILE* 3.5 33.7 - - + -
163B CYS* 3.3 31.8 - - + -
164B ALA 4.1 0.6 + - - -
176B CYS* 3.0 18.2 + - + +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ASN* 3.2 12.0 + - - -
96B TRP* 1.3 96.2 - - + +
98B SER* 1.3 60.7 + - - +
100B GLN* 3.2 6.8 + - - +
101B ARG* 3.0 25.5 + - - +
176B CYS* 4.7 8.4 + - + +
301B NAG 4.3 5.7 + - - -
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Residues in contact with SER 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.7 24.2 + - - +
95B ASN* 2.8 21.1 + - - -
97B THR* 1.3 74.6 + - - +
99B SER* 1.3 60.7 + - - +
101B ARG* 3.3 11.4 + - - +
102B PHE* 2.9 27.7 + - - +
301B NAG 2.8 35.2 + - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 3.3 21.4 - - - +
95B ASN 2.8 21.0 + - - -
96B TRP 3.6 5.4 - - - -
97B THR 3.3 0.2 - - - -
98B SER* 1.3 78.1 - - - +
100B GLN* 1.3 56.1 + - - +
102B PHE* 3.2 6.0 + - - +
103B CYS* 2.9 32.6 + - - -
110B LEU* 3.8 9.0 - - - -
132B TRP* 3.5 14.5 - - - -
182B TRP* 3.6 29.4 - - - -
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Residues in contact with GLN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B TRP* 3.0 23.3 + - + +
97B THR* 3.2 11.9 + - - +
99B SER* 1.3 76.1 - - - +
101B ARG* 1.3 55.5 + - - +
103B CYS* 3.2 2.0 + - - +
104B ASP* 2.8 39.2 + - + +
109B ASP* 2.9 26.6 + - - +
110B LEU* 2.8 43.4 + - + +
146B ILE* 3.7 24.5 - - + +
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B THR 3.0 12.8 + - - +
98B SER* 3.4 14.1 - - - +
100B GLN* 1.3 76.7 - - - +
102B PHE* 1.4 63.8 + - - +
104B ASP* 3.3 8.2 + - - +
105B SER* 3.0 22.7 + - - -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B TRP* 5.6 0.4 - + - -
88B TYR* 3.6 44.4 - + - -
94B LYS* 4.3 14.1 - - - -
98B SER 2.9 14.1 + - - +
99B SER 3.4 8.1 - - - +
101B ARG* 1.4 74.8 - - - +
103B CYS* 1.4 65.0 + - - +
105B SER* 2.6 27.5 + - - -
106B GLN* 3.3 36.0 + - + +
182B TRP* 3.4 32.8 - + + -
184B CYS* 3.9 6.1 - - - -
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Residues in contact with CYS 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B SER 2.9 22.5 + - - +
100B GLN 3.2 4.2 + - - +
102B PHE* 1.4 72.3 - - - +
104B ASP* 1.3 60.0 + - - +
106B GLN* 3.0 10.8 + - - -
108B ALA* 2.9 26.5 + - - +
109B ASP* 3.4 23.6 - - - +
110B LEU* 3.6 15.3 - - - +
182B TRP* 3.7 10.5 - - - -
184B CYS* 2.1 54.1 - - + -
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Residues in contact with ASP 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B GLN* 2.8 28.2 + - + +
101B ARG* 3.7 8.1 - - - +
103B CYS* 1.3 77.4 - - - +
105B SER* 1.3 60.8 + - - +
106B GLN 3.1 1.4 + - - -
107B ASP* 3.1 16.3 + - - +
108B ALA 3.3 12.1 + - - +
109B ASP* 5.3 1.6 - - - +
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ARG* 3.0 13.4 + - - -
102B PHE* 2.6 25.5 + - - -
104B ASP* 1.3 76.9 + - - +
106B GLN* 1.3 68.4 + - - +
107B ASP* 3.5 3.8 + - - +
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B PRO* 5.8 1.2 - - - +
79B TRP* 3.7 30.8 + - + -
88B TYR* 5.6 1.7 - - - -
102B PHE* 3.3 39.3 - - + +
103B CYS* 3.0 10.2 + - - +
105B SER* 1.3 92.6 + - - +
107B ASP* 1.3 63.5 + - - +
108B ALA* 3.3 2.4 + - - +
186B LYS* 2.7 34.9 + - - +
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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