Contacts of the helix formed by residues 87 - 109 (chain B) in PDB entry 5KAL
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 THR 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ALA* 3.6 6.6 - - + +
86B ALA* 1.3 83.7 - - - +
88B GLN* 1.3 65.3 + - - +
89B VAL* 3.0 27.8 - - + +
90B ALA* 3.4 11.8 + - - +
91B LYS* 3.2 22.9 + - - +
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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
----------------------------------------------------------
86B ALA 4.0 0.4 + - - +
87B THR* 1.3 70.4 - - - +
89B VAL* 1.3 67.9 + - + +
91B LYS* 2.8 42.4 + - - +
92B GLY* 3.1 10.9 + - - -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B THR* 3.0 27.4 - - + +
88B GLN* 1.3 79.0 - - + +
90B ALA* 1.3 64.1 + - - +
92B GLY* 3.3 6.9 + - - -
93B LEU* 2.9 22.1 + - + +
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 4.2 23.1 - - + +
87B THR* 3.4 18.6 + - - +
88B GLN 3.2 0.4 - - - -
89B VAL* 1.3 84.9 - - + +
91B LYS* 1.3 61.5 + - + +
92B GLY 3.2 0.9 + - - -
93B LEU* 3.5 22.9 + - + +
94B GLN* 3.8 18.1 + - - +
140B TYR* 5.9 0.2 - - - -
141B ARG* 6.3 0.4 - - - +
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA 5.9 0.4 - - - +
86B ALA* 4.2 11.1 + - - +
87B THR 3.2 11.9 - - - +
88B GLN* 2.8 45.9 + - + +
90B ALA* 1.3 77.8 - - + +
92B GLY* 1.3 61.2 + - - +
94B GLN* 4.1 8.5 + - - +
95B ALA* 3.7 17.0 + - - +
120B THR 4.5 11.5 + - - +
121B ARG* 4.1 26.0 - - + +
123B PRO* 4.1 14.5 - - + +
141B ARG* 4.9 9.0 - - - +
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Residues in contact with GLY 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN 3.1 11.2 + - - -
89B VAL 3.3 4.4 + - - -
90B ALA 3.1 1.0 - - - -
91B LYS* 1.3 74.6 - - - +
93B LEU* 1.3 66.2 + - - +
95B ALA* 3.1 8.2 + - - +
96B ASP* 3.1 25.1 + - - +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B VAL 2.9 29.1 + - - +
90B ALA* 3.5 16.8 + - - +
92B GLY* 1.3 72.2 - - - +
94B GLN* 1.3 64.9 + - - +
96B ASP* 2.4 35.4 + - - +
97B ILE* 3.1 6.8 + - - +
140B TYR* 4.5 17.4 - - + -
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA* 3.8 16.7 + - - +
91B LYS* 4.3 7.1 - - - +
92B GLY 3.3 0.6 - - - -
93B LEU* 1.3 76.7 - - - +
95B ALA* 1.3 64.9 + - - +
97B ILE* 3.2 8.6 - - - +
98B LEU* 2.9 34.8 + - + +
122B VAL* 5.4 0.3 - - - +
123B PRO* 3.5 29.0 - - + +
139B ALA* 2.9 34.5 + - + +
140B TYR* 3.5 31.3 + - + +
141B ARG* 3.4 29.6 + - - +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS 3.7 10.3 + - - +
92B GLY* 3.1 11.0 + - - +
94B GLN* 1.3 79.1 - - - +
96B ASP* 1.3 62.7 + - - +
98B LEU* 3.3 11.2 + - - +
99B ALA* 2.9 21.7 + - - +
116B GLU* 5.2 0.3 - - - +
118B ARG* 3.6 45.2 + - + +
123B PRO* 4.6 5.1 - - + +
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Residues in contact with ASP 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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92B GLY 3.1 8.6 + - - +
93B LEU* 2.4 35.8 + - - +
95B ALA* 1.3 76.5 - - - +
97B ILE* 1.3 83.6 + - - +
99B ALA* 2.8 29.9 + - - +
100B LYS* 3.1 11.9 + - - +
118B ARG* 4.7 5.8 - - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.9 17.2 - - + +
44B ASP* 6.0 1.6 - - + +
47B MET* 3.5 22.2 - - + -
71B VAL* 5.9 2.9 - - + -
93B LEU 3.1 8.5 + - - +
94B GLN* 3.2 16.6 - - - +
96B ASP* 1.3 91.7 + - - +
98B LEU* 1.3 66.2 + - + +
100B LYS* 3.1 16.0 + - + +
101B LEU* 3.0 23.1 + - + +
139B ALA* 4.5 12.6 - - + -
140B TYR* 3.4 29.4 - - + +
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Residues in contact with LEU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 5.6 1.1 - - + -
94B GLN* 2.9 33.3 + - + +
95B ALA* 3.6 5.8 - - - +
97B ILE* 1.3 78.7 - - + +
99B ALA* 1.3 56.7 + - - +
101B LEU* 3.8 13.3 - - + +
102B ALA* 2.9 31.2 + - - +
116B GLU* 3.9 2.6 - - - +
123B PRO* 4.2 31.9 - - + +
124B VAL 4.2 4.0 - - - +
125B VAL* 3.9 18.5 - - + +
137B ILE* 4.2 33.7 - - + +
138B THR* 4.3 16.8 - - - +
139B ALA* 4.4 9.9 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 2.9 12.3 + - - +
96B ASP* 2.8 18.3 + - - +
98B LEU* 1.3 73.6 - - - +
100B LYS* 1.3 64.1 + - + +
102B ALA* 3.2 4.0 + - - +
103B ARG* 3.0 21.7 + - - +
106B ARG* 5.0 1.0 + - - -
116B GLU* 3.2 18.8 + - - +
118B ARG* 4.5 11.4 - - - +
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Residues in contact with LYS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B VAL* 4.3 21.3 - - + -
96B ASP* 3.1 8.2 + - - +
97B ILE* 3.1 19.3 + - + +
99B ALA* 1.3 78.1 - - + +
101B LEU* 1.3 63.3 + - - +
103B ARG* 3.0 20.2 + - - +
104B VAL* 3.0 16.7 + - + +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B VAL* 5.8 0.9 - - + -
39B CYS* 4.0 10.3 - - + -
40B VAL* 3.9 32.5 - - + +
43B VAL* 3.5 28.8 - - + +
71B VAL* 4.5 8.5 - - + -
97B ILE* 3.0 16.0 + - + +
98B LEU* 3.8 15.0 - - + +
100B LYS* 1.3 75.6 - - - +
102B ALA* 1.3 63.2 + - - +
104B VAL* 3.1 4.3 + - - +
105B ILE* 2.9 36.0 + - + +
137B ILE* 3.4 37.0 - - + -
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Residues in contact with ALA 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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98B LEU 2.9 17.8 + - - +
99B ALA 3.6 4.5 - - - +
101B LEU* 1.3 76.6 - - - +
103B ARG* 1.3 62.7 + - - +
105B ILE* 3.2 14.1 + - - +
106B ARG* 2.9 36.3 + - - +
114B VAL* 4.0 20.1 - - + +
116B GLU* 3.6 20.9 - - + +
125B VAL* 4.6 5.4 - - + +
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Residues in contact with ARG 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 ALA 3.0 13.9 + - - +
100B LYS* 3.0 13.2 + - - +
102B ALA* 1.3 75.5 - - - +
104B VAL* 1.3 65.2 + - + +
106B ARG* 3.0 18.1 + - + +
107B GLN* 2.9 52.2 + - + +
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Residues in contact with VAL 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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39B CYS* 4.0 13.2 - - + +
42B ALA* 3.8 27.1 - - + +
43B VAL* 3.6 29.2 - - + +
100B LYS* 3.0 8.8 + - + +
101B LEU 3.1 6.5 + - - +
103B ARG* 1.3 76.1 - - + +
105B ILE* 1.3 64.9 + - - +
107B GLN* 3.2 8.7 + - - +
108B LYS* 2.9 39.1 + - + +
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Residues in contact with ILE 105 (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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36B VAL* 5.9 5.6 - - + -
39B CYS* 4.2 27.4 - - + -
101B LEU* 2.9 35.8 + - + +
102B ALA* 3.5 12.1 - - - +
104B VAL* 1.3 75.7 - - - +
106B ARG* 1.3 58.0 + - - +
108B LYS* 3.1 1.8 + - - -
109B HIS* 2.8 31.3 + - + +
112B TRP* 3.9 27.4 - - + -
114B VAL* 3.8 23.1 - - + -
125B VAL* 5.5 3.1 - - + -
127B VAL* 4.4 17.7 - - + -
135B PHE* 5.1 9.4 - - + -
137B ILE* 5.7 4.3 - - + -
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ALA 5.0 1.2 + - - -
102B ALA* 2.9 20.2 + - - +
103B ARG* 3.0 33.7 + - + +
105B ILE* 1.3 76.9 - - - +
107B GLN* 1.3 62.6 + - + +
109B HIS 3.0 22.7 - - - +
110B LEU* 4.1 8.8 + - - +
112B TRP 5.9 1.8 - - - +
114B VAL* 4.0 38.0 + - + +
116B GLU* 3.2 32.5 + - - +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ARG* 2.9 49.5 + - + +
104B VAL* 3.7 7.9 - - - +
106B ARG* 1.3 77.9 - - + +
108B LYS* 1.3 64.0 + - + +
109B HIS 5.0 0.2 - - - -
110B LEU* 5.3 1.2 + - - +
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Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 4.3 27.1 + - - +
39B CYS* 4.1 14.1 - - - -
42B ALA* 4.5 8.4 - - - +
104B VAL* 2.9 36.7 + - + +
105B ILE 4.0 0.4 - - - +
107B GLN* 1.3 80.1 - - + +
109B HIS* 1.3 82.3 + - + +
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Residues in contact with HIS 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LEU* 3.6 30.2 - - + +
39B CYS* 4.3 14.9 - - - -
105B ILE* 2.8 15.1 + - - +
106B ARG* 3.0 17.1 - - - +
107B GLN 3.4 0.4 - - - -
108B LYS* 1.3 98.7 + - + +
110B LEU* 1.3 62.9 + - - +
111B SER 3.6 1.3 - - - -
112B TRP* 3.4 70.7 + + + +
114B VAL* 6.0 0.2 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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