Contacts of the helix formed by residues 85 - 99 (chain B) in PDB entry 3K5N
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 ALA 85 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B ASP* 3.6 22.2 - - + +
15B THR 6.1 0.2 - - - +
18B GLY 5.3 2.5 - - - +
19B THR* 4.6 0.2 - - - -
41B SER* 4.4 2.7 - - - -
83B CYS* 3.8 3.9 - - - +
84B ARG* 1.3 82.3 - - + +
86B HIS* 1.3 65.2 + - - +
87B ARG* 5.4 0.2 - - + -
88B GLN* 3.1 31.9 + - + +
89B LEU 3.2 8.7 + - - -
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.7 30.3 - - + -
14B ASP* 3.1 7.4 + - - +
19B THR* 4.4 3.8 - - - +
41B SER* 3.2 37.1 + - - +
84B ARG 4.3 0.6 + - - -
85B ALA* 1.3 72.4 - - - +
87B ARG* 1.3 58.6 + - - +
89B LEU* 3.1 13.1 + - + +
90B MET* 2.7 55.9 + - + +
106B ALA 4.8 1.0 + - - -
108B VAL 3.3 18.7 + - - -
109B ARG* 3.2 41.0 + - - -
110B PRO* 3.6 19.4 - - + +
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 3.9 29.9 - - + -
13B ARG* 5.9 1.0 - - - +
14B ASP* 3.1 25.4 + - - +
85B ALA* 3.2 1.9 - - + -
86B HIS* 1.3 77.5 - - - +
88B GLN* 1.3 57.6 + - - +
90B MET* 3.8 17.2 - - - +
91B ASN* 2.9 24.9 + - - +
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Residues in contact with GLN 88 (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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61B GLN 4.4 4.3 - - - +
62B GLY* 2.3 35.6 + - - +
63B PHE* 4.1 0.4 - - - +
83B CYS* 2.7 28.7 - - + +
84B ARG* 3.2 7.2 - - - +
85B ALA* 3.1 24.2 + - + +
87B ARG* 1.3 75.5 - - - +
89B LEU* 1.3 60.5 + - - +
91B ASN* 2.8 13.3 - - - +
92B TYR* 2.6 60.7 + - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER* 4.0 19.3 - - - +
42B VAL 4.1 16.2 - - - +
43B ALA* 3.8 17.7 - - + -
81B LEU* 3.7 36.1 - - + +
83B CYS* 3.7 18.8 - - + -
85B ALA 3.2 6.9 + - - +
86B HIS* 3.1 25.3 + - + +
88B GLN* 1.3 88.4 - - - +
90B MET* 1.3 63.0 + - - +
91B ASN 3.0 0.9 + - - -
92B TYR* 4.2 2.0 - - - +
93B GLU* 3.0 23.9 + - + +
106B ALA* 4.5 14.6 - - + +
108B VAL 5.7 0.2 - - - +
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Residues in contact with MET 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B TRP* 4.6 12.3 - - - -
86B HIS* 2.7 56.4 + - + +
87B ARG* 3.8 20.0 - - - +
89B LEU* 1.3 76.8 - - - +
91B ASN* 1.3 61.4 + - - +
93B GLU* 3.4 21.6 - - - +
94B LYS* 3.7 5.9 + - - +
106B ALA 5.1 4.5 - - - +
109B ARG* 3.7 30.1 - - - +
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Residues in contact with ASN 91 (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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60B GLU* 5.7 0.6 + - - -
87B ARG 2.9 14.6 - - - +
88B GLN* 2.8 18.6 + - - +
90B MET* 1.3 79.7 - - - +
92B TYR* 1.3 79.9 + - - -
93B GLU 3.2 0.2 - - - -
94B LYS* 3.0 29.0 - - - +
95B ARG* 3.3 13.5 + - - +
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Residues in contact with TYR 92 (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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57B LEU* 3.7 28.5 - - + -
60B GLU* 2.3 45.7 + - + +
61B GLN 4.1 6.4 + - - -
63B PHE* 3.6 23.0 - + - -
81B LEU* 4.5 13.0 - - + -
83B CYS* 4.0 24.0 - - - -
88B GLN* 2.6 40.0 + - + +
89B LEU* 3.1 4.0 + - - +
91B ASN* 1.3 86.7 + - - +
93B GLU* 1.3 59.2 + - - +
95B ARG* 2.5 35.7 + - - +
96B LEU* 2.7 17.9 + - + +
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Residues in contact with GLU 93 (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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43B ALA* 5.6 0.7 - - + -
81B LEU* 5.6 1.8 - - + +
89B LEU* 3.0 13.5 + - + +
90B MET* 3.4 16.4 - - - +
91B ASN 3.2 0.2 - - - -
92B TYR* 1.3 79.6 - - - +
94B LYS* 1.3 59.7 + - - +
96B LEU* 3.8 8.8 - - - +
97B ARG* 2.6 55.7 + - - +
103B VAL* 3.9 26.6 - - + +
106B ALA* 3.9 30.8 - - + +
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Residues in contact with LYS 94 (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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90B MET 3.7 6.0 + - - +
91B ASN* 3.0 22.2 + - - +
92B TYR 3.0 0.6 - - - -
93B GLU* 1.3 92.0 + - - +
95B ARG* 1.3 69.2 + - + +
97B ARG* 3.7 15.0 - - - +
98B GLU* 2.8 63.0 + - - +
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Residues in contact with ARG 95 (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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56B ILE* 4.0 32.8 + - + +
57B LEU* 3.9 19.5 - - + +
58B GLN 5.7 0.2 + - - -
60B GLU* 2.5 41.0 + - - -
91B ASN* 3.8 19.6 + - - +
92B TYR* 2.5 20.4 + - - +
94B LYS* 1.3 85.4 - - + +
96B LEU* 1.3 59.3 + - + +
98B GLU* 3.3 9.1 + - - +
99B GLY* 2.8 27.0 + - - -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ILE* 4.0 27.4 - - + -
53B ALA* 4.2 22.0 - - + +
56B ILE* 3.7 36.1 - - + -
57B LEU* 4.3 17.3 - - + -
81B LEU* 4.5 11.0 - - + -
92B TYR* 2.7 25.9 + - + +
93B GLU 3.8 3.1 - - - +
95B ARG* 1.3 73.6 - - - +
97B ARG* 1.3 59.6 + - - +
99B GLY 3.2 6.1 + - - +
100B GLY 3.3 0.2 + - - -
101B VAL* 2.8 37.3 + - + +
103B VAL* 4.0 17.0 - - + -
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Residues in contact with ARG 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B GLU* 2.6 42.4 + - - +
94B LYS* 3.7 19.8 - - - +
96B LEU* 1.3 74.4 - - - +
98B GLU* 1.3 76.6 + - - +
99B GLY 3.1 1.3 + - - -
100B GLY* 3.4 11.3 + - - -
101B VAL 3.6 12.5 + - - +
103B VAL* 5.6 4.3 - - + -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B LYS* 2.8 52.4 + - - +
95B ARG* 3.5 7.3 - - - +
97B ARG* 1.3 94.6 + - - +
99B GLY* 1.3 57.7 + - - +
100B GLY 3.4 0.8 + - - -
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Residues in contact with GLY 99 (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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52B ARG* 2.6 39.3 + - - -
56B ILE* 4.0 14.7 - - - +
95B ARG 2.8 14.8 + - - -
96B LEU 3.2 2.4 + - - -
97B ARG 3.1 0.4 - - - -
98B GLU* 1.3 80.6 - - - +
100B GLY* 1.3 57.5 + - - +
101B VAL 3.6 2.0 + - - -
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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