Contacts of the helix formed by residues 95 - 116 (chain D) in PDB entry 1KFY
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 95 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D VAL 3.2 0.6 + - - -
94D PRO* 1.3 75.0 - - - +
96D GLY* 1.3 66.8 + - - +
97D LYS 3.1 3.1 - - - -
98D TRP* 2.8 27.1 + - + -
99D VAL* 2.8 13.0 + - + +
239N THR* 3.4 41.5 + - + -
240N LEU* 3.8 13.2 - - + +
243N ARG* 5.4 0.4 - - - +
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Residues in contact with GLY 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D HIS* 4.3 9.4 - - - -
93D VAL* 2.7 34.7 + - - -
95D ALA* 1.3 74.8 - - - +
97D LYS* 1.3 62.3 + - - +
99D VAL* 2.9 13.0 + - - +
100D PHE* 2.9 25.2 + - - +
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Residues in contact with LYS 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B GLN* 5.0 4.2 + - - -
9D ASP* 3.2 31.8 + - - -
10D GLU* 3.8 17.7 + - - +
13D PHE* 3.2 27.6 - - - -
83D HIS* 4.1 20.2 - - + +
95D ALA 3.0 1.2 + - - -
96D GLY* 1.3 73.1 - - - +
98D TRP* 1.3 66.6 + - + +
100D PHE* 5.4 0.2 - - - -
101D TYR* 3.0 51.6 + - + +
710D CE1 3.8 44.1 - - - +
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Residues in contact with TRP 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ALA* 2.8 19.1 + - + +
97D LYS* 1.3 75.1 - - + +
99D VAL* 1.3 68.7 + - - +
102D GLY* 2.8 22.4 + - - +
710D CE1 3.2 111.9 - - + +
235N PHE* 5.3 2.8 - + - -
239N THR* 3.9 27.2 + - + +
12P VAL* 3.9 28.0 - - + -
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D VAL* 4.5 8.5 - - + -
94D PRO 3.5 16.2 - - - +
95D ALA* 2.8 21.3 + - + +
96D GLY* 2.9 10.0 + - - +
98D TRP* 1.3 81.4 - - - +
100D PHE* 1.3 74.5 + - + +
103D LEU* 2.8 33.3 + - + +
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Residues in contact with PHE 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D LEU* 3.7 42.3 - - + +
82D MET* 3.8 24.9 - - + -
83D HIS* 3.8 31.2 - - + -
86D MET* 3.9 33.7 - - + -
93D VAL* 4.2 18.2 - - + -
96D GLY* 2.9 25.7 + - - +
97D LYS 4.5 0.4 - - - +
99D VAL* 1.3 85.1 - - + +
101D TYR* 1.3 66.1 + - + +
103D LEU* 3.4 10.0 + - + +
104D ALA* 3.1 20.4 + - - +
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Residues in contact with TYR 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D GLU* 4.1 2.1 + - - -
13D PHE* 3.3 56.7 - + + +
76D TRP* 3.4 24.3 - + + -
79D LEU* 5.1 1.8 - - + -
80D HIS* 2.8 50.3 + - + -
83D HIS* 3.7 26.7 - + + -
97D LYS* 3.0 42.9 + - + +
100D PHE* 1.3 76.4 - - + +
102D GLY* 1.3 57.2 + - - +
104D ALA* 3.3 6.7 - - + +
105D ALA* 2.9 24.8 + - - +
710D CE1 3.6 20.0 - - + +
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TRP 2.8 21.7 + - - -
101D TYR* 1.3 74.8 - - - +
103D LEU* 1.3 66.7 + - - +
104D ALA 3.0 0.9 - - - -
105D ALA* 2.9 4.0 + - - +
106D ILE* 2.8 32.2 + - - +
710D CE1 3.7 24.1 - - - +
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Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D LEU* 4.1 25.1 - - + -
99D VAL* 2.8 23.3 + - + +
100D PHE* 3.6 9.2 - - + +
102D GLY* 1.3 73.5 - - - +
104D ALA* 1.3 56.8 + - - +
106D ILE* 3.2 14.9 + - + +
107D LEU* 2.9 54.4 + - + +
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Residues in contact with ALA 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D LEU* 5.0 4.8 - - + +
76D TRP* 3.3 34.1 - - + +
79D LEU* 3.6 25.3 - - + +
100D PHE 3.1 6.9 + - - +
101D TYR* 3.3 11.0 - - + +
102D GLY 3.0 0.6 - - - -
103D LEU* 1.3 79.1 - - - +
105D ALA* 1.3 54.3 + - - +
107D LEU* 3.4 4.6 + - - +
108D THR* 2.5 39.3 + - - -
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Residues in contact with ALA 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TRP* 3.5 11.6 - - + -
101D TYR 2.9 13.0 + - - +
102D GLY 2.9 7.5 + - - +
104D ALA* 1.3 76.4 - - - +
106D ILE* 1.3 64.0 + - - +
108D THR* 3.1 8.4 + - - -
109D VAL* 2.8 29.4 + - + +
710D CE1 3.8 29.8 - - + -
810P CE1 5.4 5.4 - - - -
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D GLY* 2.8 23.9 + - - +
103D LEU* 3.4 17.9 - - + +
105D ALA* 1.3 71.2 - - - +
107D LEU* 1.3 74.0 + - + +
109D VAL* 2.9 9.8 + - - +
110D VAL* 2.8 35.4 + - + +
710D CE1 3.9 25.3 - - + +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ILE* 3.8 28.9 - - + -
43C ILE* 4.6 14.1 - - + +
75D LEU* 3.8 34.8 - - + -
79D LEU* 5.2 0.7 - - + -
103D LEU* 2.9 44.0 + - + +
104D ALA 3.8 0.9 - - - +
106D ILE* 1.3 81.2 - - + +
108D THR* 1.3 52.3 + - - +
110D VAL* 3.3 13.1 - - + +
111D THR* 2.7 39.7 + - - -
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Residues in contact with THR 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D PHE* 3.9 15.6 - - + -
72D VAL* 3.7 28.9 - - + +
75D LEU* 5.1 1.2 - - - +
76D TRP* 3.0 20.1 + - - -
104D ALA 2.5 23.1 + - - -
105D ALA* 3.1 12.4 - - - -
107D LEU* 1.3 76.0 - - - +
109D VAL* 1.3 54.9 + - + +
111D THR* 3.0 5.0 + - - -
112D LEU* 2.7 35.9 + - + +
810P CE1 4.2 16.2 - - - +
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Residues in contact with VAL 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D ALA* 2.8 16.3 + - + +
106D ILE* 3.3 10.1 - - - +
108D THR* 1.3 78.4 - - + +
110D VAL* 1.3 58.5 + - + +
112D LEU* 2.5 32.7 + - + +
113D ILE* 2.8 23.4 + - + +
710D CE1 5.8 7.0 - - + -
109P VAL* 4.4 29.6 - - + -
112P LEU* 3.8 28.5 - - + -
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Residues in contact with VAL 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 4.4 13.9 - - + -
47C PHE* 3.7 27.3 - - + -
106D ILE* 2.8 35.1 + - + +
107D LEU* 3.3 18.4 - - + +
109D VAL* 1.3 73.4 - - + +
111D THR* 1.3 64.5 + - - +
113D ILE* 3.1 14.9 + - + +
114D GLY 3.0 17.2 + - - -
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Residues in contact with THR 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43C ILE* 3.5 23.5 - - - +
46C LEU* 4.6 5.3 - - + +
47C PHE* 5.3 1.3 - - - -
68D PHE* 3.4 36.1 - - + -
71D ILE* 3.6 21.0 - - + +
72D VAL* 4.0 9.8 - - + +
75D LEU* 5.4 0.2 - - - +
107D LEU 2.7 20.2 + - - -
108D THR 3.2 8.5 - - - -
110D VAL* 1.3 74.3 - - - +
112D LEU* 1.3 63.6 + - - +
114D GLY* 3.1 3.5 + - - +
115D VAL* 2.9 25.2 + - + +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68D PHE* 4.3 23.3 - - + -
108D THR* 2.7 13.0 + - + +
109D VAL* 2.5 22.0 + - + +
111D THR* 1.3 74.2 - - - +
113D ILE* 1.3 61.2 + - + +
115D VAL* 3.3 17.4 + - + +
116D VAL* 2.9 36.9 + - + +
109P VAL* 4.0 25.6 - - + -
113P ILE* 5.0 7.0 - - + -
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Residues in contact with ILE 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C PHE* 5.1 6.5 - - + -
109D VAL* 2.8 30.4 + - + +
110D VAL* 3.4 13.0 - - + +
112D LEU* 1.3 75.5 - - + +
114D GLY* 1.3 65.6 + - - +
116D VAL* 2.9 27.5 + - + +
117D THR* 3.1 8.5 + - - -
118D ILE* 5.1 10.8 - - + -
109P VAL* 5.9 0.9 - - + -
112P LEU* 4.5 16.6 - - + -
113P ILE* 3.9 23.3 - - + -
116P VAL* 4.8 21.5 - - + -
117P THR* 5.7 1.3 - - - +
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Residues in contact with GLY 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C LEU* 4.3 18.9 - - - +
47C PHE* 3.6 30.2 - - - -
50C LYS* 5.1 1.9 - - - +
110D VAL 3.0 7.7 + - - -
111D THR 3.1 3.8 + - - -
113D ILE* 1.3 79.7 - - - +
115D VAL* 1.3 58.6 + - - +
117D THR* 3.1 21.1 - - - +
118D ILE* 3.4 6.3 + - - -
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C LEU* 4.0 20.2 - - + -
64D ARG* 2.5 67.3 + - + +
67D LEU* 4.4 7.4 - - + -
68D PHE* 4.3 20.0 - - + +
111D THR* 2.9 18.8 + - + +
112D LEU* 3.3 26.7 - - + +
114D GLY* 1.3 74.6 - - - +
116D VAL* 1.3 54.2 + - + +
117D THR* 2.7 7.4 - - - +
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Residues in contact with VAL 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D ARG* 3.5 5.0 + - - +
112D LEU* 2.9 30.5 + - + +
113D ILE* 2.9 27.8 - - + +
115D VAL* 1.3 75.8 - - + +
117D THR* 1.3 76.5 + - - +
113P ILE* 4.0 25.1 - - + -
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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
------------------------------------------------------------
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