Contacts of the helix formed by residues 89 - 99 (chain A) in PDB entry 3KCN
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 89 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A MSE 3.4 35.8 - - + +
59A ARG* 3.8 21.5 + - - +
85A THR* 3.2 19.1 - - - +
86A GLY 2.8 18.6 + - - +
88A GLN* 1.3 86.3 - - - +
90A LEU* 1.3 65.2 + - - +
91A THR 3.1 3.7 + - - -
92A THR* 3.1 17.4 + - - -
93A ALA* 3.2 9.7 + - - +
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Residues in contact with LEU 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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85A THR* 4.3 2.2 + - + -
86A GLY 3.7 3.9 + - - +
87A ASN 3.7 14.3 + - - +
88A GLN 3.5 2.4 - - - -
89A ASP* 1.3 75.0 - - - +
91A THR* 1.3 60.2 + - - +
93A ALA* 3.1 5.9 + - - +
94A MSE 2.8 57.9 + - + +
105A PHE* 3.6 25.1 - - + -
107A ASN* 4.4 12.1 - - - +
90B LEU* 4.0 21.8 - - + -
91B THR* 5.5 10.5 - - + -
94B MSE 4.4 7.6 - - - -
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Residues in contact with THR 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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88A GLN 5.2 1.3 + - - -
89A ASP 3.1 1.0 + - - -
90A LEU* 1.3 80.3 - - - +
92A THR* 1.3 62.1 + - - +
94A MSE 3.3 7.4 + - + +
95A GLU* 3.1 33.4 + - + +
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Residues in contact with THR 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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58A MSE 3.5 29.2 - - + +
66A THR* 4.4 17.4 + - + +
88A GLN 5.4 0.3 + - - -
89A ASP* 3.1 8.9 + - - -
91A THR* 1.3 80.5 - - - +
93A ALA* 1.3 58.0 + - - +
95A GLU* 3.4 20.7 + - - +
96A ALA* 3.3 24.3 + - - +
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Residues in contact with ALA 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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58A MSE 3.8 7.4 - - + +
83A MSE 5.4 5.2 - - + -
85A THR* 3.8 24.2 - - + +
89A ASP 3.2 4.5 + - - +
90A LEU* 3.1 10.9 + - - +
92A THR* 1.3 75.4 - - - +
94A MSE 1.3 60.6 + - - +
96A ALA* 3.5 5.3 + - - +
97A VAL* 3.0 31.9 + - - +
102A VAL* 4.7 2.3 - - + +
105A PHE* 3.8 29.7 - - + -
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Residues in contact with MSE 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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90A LEU* 2.8 50.5 + - + +
91A THR* 3.3 7.4 + - - +
93A ALA* 1.3 77.5 - - - +
95A GLU* 1.3 58.3 + - - +
97A VAL* 3.2 10.3 + - - +
98A ASN* 3.0 46.1 + - - +
105A PHE* 3.8 18.6 - - + -
90B LEU* 3.8 22.0 - - + -
94B MSE 4.4 1.8 - - - +
105B PHE* 4.5 28.5 - - + +
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Residues in contact with GLU 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 THR* 3.1 19.9 + - + +
92A THR* 3.4 30.2 + - - +
94A MSE 1.3 75.5 - - - +
96A ALA* 1.3 61.0 + - + +
98A ASN* 3.8 9.1 - - - +
99A GLU* 3.0 34.7 + - + +
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Residues in contact with ALA 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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66A THR* 4.8 12.8 - - - +
83A MSE 5.5 2.7 - - - -
92A THR 3.3 17.2 + - - +
93A ALA* 3.6 6.1 - - - +
94A MSE 3.1 0.4 - - - -
95A GLU* 1.3 80.9 - - + +
97A VAL* 1.3 63.6 + - - +
99A GLU* 3.4 1.2 + - - +
100A GLY 3.4 2.9 + - - -
101A GLN* 3.0 40.2 + - + +
102A VAL* 3.1 27.4 + - + -
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Residues in contact with VAL 97 (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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93A ALA 3.0 20.1 + - - +
94A MSE 3.5 11.9 - - - +
96A ALA* 1.3 74.9 - - - +
98A ASN* 1.3 60.0 + - - +
100A GLY* 2.8 22.7 + - - -
102A VAL* 3.3 32.7 - - + +
103A PHE 4.7 8.7 - - - +
104A ARG* 4.7 1.6 - - - +
105A PHE* 3.8 24.5 - - + +
103B PHE 4.5 4.5 - - - +
104B ARG* 3.3 35.2 + - + +
105B PHE 5.8 1.1 - - - +
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Residues in contact with ASN 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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94A MSE 3.0 35.6 + - - +
95A GLU* 4.0 8.2 - - - +
96A ALA 3.3 0.2 - - - -
97A VAL* 1.3 73.8 - - - +
99A GLU* 1.3 65.2 + - - +
100A GLY 3.0 5.9 + - - -
104B ARG* 3.3 37.9 + - - +
105B PHE 3.5 20.7 + - - +
106B LEU* 4.5 12.2 - - - +
114B ASP* 5.9 5.4 - - + +
117B ALA* 5.4 8.3 - - - +
118B ALA* 5.2 1.4 - - - +
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Residues in contact with GLU 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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73A ARG* 5.1 2.9 + - - -
95A GLU* 3.0 19.9 + - + +
96A ALA 3.9 1.3 - - - +
97A VAL 3.3 0.6 - - - -
98A ASN* 1.3 79.5 - - - +
100A GLY* 1.3 59.9 + - - +
101A GLN* 3.7 35.0 + - - +
114B ASP* 5.6 2.1 - - - +
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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