Contacts of the helix formed by residues 86 - 103 (chain B) in PDB entry 1KEK
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 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ILE* 3.5 15.6 - - + +
31B THR 4.5 2.2 - - - +
32B PRO* 4.4 6.1 - - + -
33B SER* 4.4 0.7 - - - +
85B THR* 1.3 86.1 + - - +
87B SER* 1.3 76.2 - - - +
88B GLN 3.3 0.7 + - - -
89B GLY* 2.8 16.1 + - - -
90B LEU* 3.1 6.5 + - - -
111B VAL* 4.4 2.2 - - - -
112B THR* 3.2 27.4 - - - +
114B ARG* 4.2 5.2 - - + -
129B ASP* 3.6 7.0 - - - -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 4.5 0.2 - - - -
86B ALA* 1.3 74.1 - - - +
88B GLN* 1.3 75.4 + - - +
90B LEU* 3.0 17.7 + - - +
91B LEU* 3.1 14.2 + - - +
114B ARG* 3.3 42.3 + - - -
115B ALA 2.8 21.9 + - - -
116B ILE* 3.6 7.3 - - - +
129B ASP* 2.6 29.2 + - - +
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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
----------------------------------------------------------
95A PRO* 4.6 8.8 + - - +
30B ILE* 4.2 2.0 - - + +
86B ALA 3.3 0.2 + - - -
87B SER* 1.3 90.8 + - - +
89B GLY* 1.3 62.1 + - - +
91B LEU* 3.4 22.9 + - - +
92B LEU* 3.2 27.4 + - - +
114B ARG* 4.4 9.5 + - - +
115B ALA 4.3 0.2 - - - +
116B ILE* 3.5 6.6 - - - +
117B ALA* 2.7 42.7 + - - +
121B LEU* 5.5 3.5 - - + +
868B LEU* 3.7 24.7 - - + +
870B GLU* 5.3 3.8 + - - +
3236B HTL 3.6 38.2 - - + +
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Residues in contact with GLY 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.7 3.6 - - - +
64B GLU* 3.3 49.2 - - - +
85B THR* 3.5 9.6 - - - -
86B ALA 2.8 10.5 + - - -
88B GLN* 1.3 78.9 - - - +
90B LEU* 1.3 60.7 + - - -
92B LEU 3.1 10.2 + - - -
93B MET* 3.3 5.4 + - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B THR* 3.6 26.1 + - + -
86B ALA* 3.1 10.9 + - - -
87B SER 3.0 9.6 + - - +
89B GLY* 1.3 76.6 - - - +
91B LEU* 1.3 65.1 + - + +
93B MET* 3.0 14.6 + - + +
94B ILE* 3.2 12.6 + - + +
97B MET* 3.8 26.0 - - + -
109B PHE* 4.2 11.2 - - + -
111B VAL* 4.3 11.2 - - + -
129B ASP* 3.6 34.5 - - + +
130B ILE* 4.0 5.8 - - + +
133B ALA* 4.3 9.0 - - + -
168B MET* 4.0 19.3 - - - -
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Residues in contact with LEU 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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91A LEU 5.3 4.5 - - - +
94A ILE* 4.6 5.7 - - + +
95A PRO* 4.2 28.6 - - + +
98A TYR* 4.0 21.5 - - + -
87B SER 3.1 12.4 + - - +
88B GLN* 3.7 23.3 - - - +
89B GLY 3.3 0.4 - - - -
90B LEU* 1.3 76.4 - - + +
92B LEU* 1.3 62.9 + - - +
94B ILE* 3.2 32.8 + - + +
95B PRO* 4.0 3.5 - - - +
116B ILE* 3.6 27.8 - - + -
129B ASP* 4.9 3.4 - - - +
132B ALA* 3.6 31.0 - - + -
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Residues in contact with LEU 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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65A ALA* 6.3 2.9 - - + -
92A LEU* 6.0 5.3 - - + +
95A PRO* 4.3 13.2 - - + -
63B SER* 4.4 5.8 - - - +
64B GLU* 3.8 9.4 - - + +
65B ALA* 3.6 41.0 - - + +
68B ALA* 5.0 0.2 - - - +
88B GLN 3.2 13.2 + - - +
89B GLY 3.1 9.3 + - - +
91B LEU* 1.3 76.1 - - - +
93B MET* 1.3 60.5 + - - +
94B ILE 3.3 0.4 + - - -
95B PRO* 3.8 10.7 - - - +
96B ASN* 5.4 1.0 + - - -
870B GLU* 3.7 25.4 - - + +
969B ILE* 4.1 13.9 - - + -
3236B HTL 3.5 24.5 - - + -
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Residues in contact with MET 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B TYR* 6.0 0.4 - - + -
64B GLU* 3.5 38.8 - - + +
67B ALA* 4.3 6.1 - - + -
68B ALA* 3.6 16.4 - - + -
83B THR* 3.9 26.7 - - + +
84B PHE 4.8 0.7 - - - +
85B THR* 3.6 32.8 - - - +
89B GLY 3.5 8.7 - - - +
90B LEU* 3.0 9.7 + - - +
92B LEU* 1.3 79.8 - - - +
94B ILE* 1.3 64.7 + - - +
95B PRO* 3.5 1.3 - - - -
96B ASN* 3.2 7.6 + - - +
97B MET* 2.9 23.5 + - - +
109B PHE* 3.4 33.7 - - + -
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.5 14.4 - - + +
94A ILE* 5.3 14.8 - - + -
132A ALA* 5.8 1.3 - - + -
90B LEU* 3.2 12.0 + - + +
91B LEU* 3.2 38.3 + - + +
93B MET* 1.3 76.1 - - - +
95B PRO* 1.3 68.5 - - + +
97B MET* 3.0 18.4 + - - +
98B TYR* 3.3 36.0 + - + +
132B ALA* 3.6 26.0 - - + +
133B ALA* 4.3 15.5 - - + -
135B GLN* 6.2 0.2 - - - +
136B THR* 4.0 5.2 - - + -
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Residues in contact with PRO 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 4.4 8.6 + - - +
91A LEU* 3.9 37.9 - - + +
92A LEU* 4.1 20.0 - - + -
116A ILE* 5.6 0.2 - - - +
117A ALA 4.8 0.7 - - - +
868A LEU* 3.6 24.4 - - + +
870A GLU* 3.9 5.4 - - - +
91B LEU 4.0 4.5 - - - +
92B LEU 3.8 12.1 - - - +
93B MET 3.6 3.8 - - - -
94B ILE* 1.3 96.2 - - + +
96B ASN* 1.4 60.9 + - - +
98B TYR* 3.4 13.0 + - + +
99B LYS* 3.5 13.7 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A SER* 3.1 6.8 + - - -
868A LEU* 3.6 12.9 - - - +
870A GLU* 6.1 0.2 - - - +
871A ASP* 3.2 21.1 + - - +
65B ALA* 4.1 8.1 + - - +
68B ALA* 3.6 34.0 - - + +
69B GLY* 3.4 14.9 - - - +
72B HIS* 3.1 31.5 + - - +
92B LEU 5.4 0.8 + - - -
93B MET 3.2 2.4 + - - +
95B PRO* 1.4 78.9 - - - +
97B MET* 1.3 58.2 + - - +
99B LYS* 3.1 5.5 + - - +
100B ILE* 2.9 34.7 + - + +
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B LEU* 3.8 25.8 - - + -
93B MET 2.9 24.0 + - - +
94B ILE* 3.0 13.4 + - - +
96B ASN* 1.3 75.8 - - - +
98B TYR* 1.3 63.3 + - - +
100B ILE* 3.4 1.1 + - - -
101B SER* 3.0 25.2 + - - -
109B PHE* 3.5 22.9 - - + -
133B ALA* 3.9 18.8 - - + -
136B THR* 3.6 26.2 - - - +
138B PHE* 3.3 41.2 - - + -
168B MET* 4.0 12.1 - - + -
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Residues in contact with TYR 98 (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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91A LEU* 4.0 15.7 - - + -
116A ILE* 3.5 27.4 - - + -
117A ALA 3.6 16.4 - - - +
118A ALA* 3.4 10.4 - - + +
128A GLN* 4.5 6.7 + - + -
132A ALA* 3.5 16.6 - - + +
94B ILE* 3.3 43.5 + - + +
95B PRO 3.6 5.8 - - - +
96B ASN 3.3 0.4 - - - -
97B MET* 1.3 78.9 - - - +
99B LYS* 1.3 59.1 + - - +
101B SER* 3.3 1.2 + - - -
102B GLY* 2.8 27.0 + - - -
135B GLN* 3.3 41.4 - - + +
136B THR* 3.8 24.2 - - + -
229B ARG* 4.5 18.6 - - - -
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Residues in contact with LYS 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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117A ALA* 3.7 31.0 - - - +
118A ALA 3.6 18.4 + - - +
120A ALA 4.9 0.2 - - - -
121A LEU 4.8 5.1 - - - +
866A ASN* 3.0 28.9 + - - +
867A SER* 3.0 22.5 + - - +
868A LEU* 4.1 15.3 - - + -
72B HIS* 3.7 23.3 - - + +
95B PRO 3.5 4.2 + - - +
96B ASN* 3.1 10.8 + - - +
98B TYR* 1.3 78.9 - - - +
100B ILE* 1.3 56.1 + - - +
103B GLU* 2.8 53.8 + - - +
217B GLY* 3.8 17.4 - - - -
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Residues in contact with ILE 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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68B ALA 4.1 17.3 - - - +
71B VAL* 4.2 8.1 - - + -
72B HIS* 3.8 23.6 - - + -
75B LEU* 4.0 20.6 - - + -
96B ASN* 2.9 26.2 + - + +
97B MET 3.9 3.4 - - - +
99B LYS* 1.3 76.2 - - - +
101B SER* 1.3 59.6 + - - +
103B GLU 3.5 0.5 + - - -
104B LEU 3.4 3.1 + - - -
105B LEU* 3.1 38.5 + - + +
107B GLY* 4.6 1.1 - - - +
109B PHE* 4.0 29.8 - - + -
138B PHE* 3.8 17.0 - - + -
166B PRO* 3.9 12.1 - - + -
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Residues in contact with SER 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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333A PRO* 6.0 0.2 - - - +
97B MET 3.0 11.0 + - - -
98B TYR 3.3 3.5 + - - -
100B ILE* 1.3 72.7 - - - +
102B GLY* 1.3 68.4 + - - +
103B GLU 3.0 1.8 - - - -
104B LEU* 2.9 26.2 + - - +
136B THR 2.5 25.7 + - - -
137B GLY* 3.5 15.7 - - - -
138B PHE* 4.2 0.4 - - - -
166B PRO* 3.6 18.1 - - - +
229B ARG* 5.7 2.1 + - - -
236B TYR* 3.5 22.8 + - - -
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Residues in contact with GLY 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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118A ALA* 3.7 18.4 - - - -
119A HIS* 3.6 21.6 - - - +
661A ALA 4.0 3.3 - - - +
662A ASP* 3.8 8.8 - - - -
98B TYR 2.8 22.1 + - - -
99B LYS 3.6 0.4 - - - -
101B SER* 1.3 77.9 + - - +
103B GLU* 1.4 62.4 - - - +
104B LEU* 3.7 2.1 + - - +
229B ARG* 5.0 6.3 - - - -
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Residues in contact with GLU 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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118A ALA 4.2 7.2 - - - +
119A HIS* 4.8 2.7 - - - +
662A ASP* 3.4 30.0 - - + +
866A ASN 4.3 2.6 - - - +
875A TYR* 4.7 0.2 + - - -
72B HIS* 2.8 30.6 + - - -
99B LYS* 2.8 34.8 + - - +
100B ILE 4.3 0.2 - - - +
101B SER 3.0 0.2 - - - -
102B GLY* 1.4 79.6 - - - +
104B LEU* 1.3 69.0 + - - +
105B LEU* 3.4 13.0 + - + +
206B LYS* 4.4 2.6 + - - -
216B ARG* 2.8 44.7 + - + +
217B GLY* 4.2 15.0 + - - +
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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