Contacts of the helix formed by residues 102 - 120 (chain H) in PDB entry 1KX4
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 GLU 102 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92G GLU* 3.3 11.7 - - + +
100H PRO 3.2 0.8 + - - -
101H GLY* 1.3 76.6 - - - +
103H LEU* 1.3 62.7 + - - +
104H ALA 3.0 4.5 - - - +
105H LYS* 3.3 43.4 + - - +
106H HIS* 3.3 44.4 + - + -
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Residues in contact with LEU 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 3.2 30.4 - - + +
58G LEU* 3.8 20.2 - - + -
61G GLU* 3.9 31.0 - - + +
90G ASP* 5.6 0.7 - - - +
92G GLU* 3.1 37.6 + - + +
93G LEU* 3.9 22.2 - - + -
96G LEU* 4.6 4.9 - - + -
99H LEU* 3.9 6.0 - - + +
100H PRO* 3.6 20.2 - - + +
102H GLU* 1.3 79.9 - - - +
104H ALA* 1.3 56.0 + - - +
106H HIS* 5.8 0.2 - - - +
107H ALA* 3.1 24.3 + - - +
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Residues in contact with ALA 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95H VAL* 4.0 12.1 - - + +
96H ARG* 4.4 12.1 - - + +
99H LEU* 3.9 30.7 - - + +
100H PRO 3.4 8.7 + - - +
101H GLY* 4.9 2.5 - - - -
102H GLU 3.0 3.1 - - - +
103H LEU* 1.3 78.4 - - - +
105H LYS* 1.3 60.4 + - - +
106H HIS 3.2 0.2 - - - -
107H ALA* 3.8 0.6 - - - +
108H VAL* 2.8 38.9 + - + +
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Residues in contact with LYS 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H GLU* 3.3 35.8 + - - +
104H ALA* 1.3 77.9 - - - +
106H HIS* 1.3 79.0 + - + +
108H VAL* 3.4 7.7 + - - +
109H SER* 3.0 28.7 + - - -
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Residues in contact with HIS 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G TYR* 2.9 38.9 + + + +
102H GLU* 3.3 24.8 + - + +
104H ALA 3.2 0.4 - - - -
105H LYS* 1.3 99.6 + - + +
107H ALA* 1.3 58.3 + - - +
109H SER* 3.2 8.8 + - - -
110H GLU* 2.9 35.1 + - + +
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Residues in contact with ALA 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54G VAL* 3.8 30.7 - - + +
57G TYR* 3.5 23.7 - - + -
95H VAL* 4.0 5.2 - - + -
99H LEU* 3.9 10.8 - - + -
103H LEU 3.1 20.9 + - - +
104H ALA 3.8 2.5 - - - +
106H HIS* 1.3 75.1 - - - +
108H VAL* 1.3 55.0 + - - +
110H GLU* 3.2 2.6 + - - +
111H GLY* 2.7 34.8 + - - -
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.4 19.8 + - - +
92H GLN* 4.1 8.5 - - + +
95H VAL* 4.0 12.1 - - + +
96H ARG* 3.7 48.7 - - + +
104H ALA 2.8 28.1 + - - +
105H LYS* 3.4 7.9 - - - +
107H ALA* 1.3 77.7 - - - +
109H SER* 1.3 58.1 + - - +
112H THR* 2.9 40.0 + - + +
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Residues in contact with SER 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H LYS* 3.0 16.6 + - - -
106H HIS* 3.3 11.8 + - - -
107H ALA 3.2 0.2 - - - -
108H VAL* 1.3 75.3 - - - +
110H GLU* 1.3 74.2 + - - +
111H GLY 3.2 0.2 - - - -
112H THR* 3.1 8.1 + - - -
113H LYS* 3.0 30.0 + - - +
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Residues in contact with GLU 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G LEU* 5.5 0.3 - - - +
53G ALA* 3.6 11.4 - - + +
57G TYR* 4.3 29.2 - - + -
106H HIS* 2.9 23.0 + - + +
107H ALA 3.8 3.6 - - - +
109H SER* 1.3 87.9 + - - +
111H GLY* 1.3 65.0 + - - +
113H LYS* 3.6 24.1 + - - +
114H ALA* 3.0 24.9 + - - +
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Residues in contact with GLY 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.8 25.7 - - - -
53G ALA* 3.9 14.1 - - - +
54G VAL* 4.7 0.7 - - - -
107H ALA 2.7 16.8 + - - -
108H VAL 3.8 0.9 - - - -
110H GLU* 1.3 75.7 - - - +
112H THR* 1.3 63.8 + - - +
114H ALA* 3.0 12.3 + - - +
115H VAL* 3.1 17.5 + - - +
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Residues in contact with THR 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 3.6 6.6 - - + +
92H GLN* 3.4 26.0 - - - +
108H VAL* 2.9 32.3 + - + +
109H SER* 3.1 12.1 + - - -
111H GLY* 1.3 72.5 - - - +
113H LYS* 1.3 64.0 + - - +
115H VAL* 3.4 4.6 + - - +
116H THR* 3.0 32.0 + - - -
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Residues in contact with LYS 113 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109H SER 3.0 17.6 + - - +
110H GLU* 3.8 25.5 + - - +
112H THR* 1.3 81.7 + - - +
114H ALA* 1.3 62.2 + - - +
116H THR* 3.6 6.6 + - - +
117H LYS* 3.2 28.7 + - + +
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Residues in contact with ALA 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ALA* 3.8 15.2 - - - +
23G LEU* 4.0 15.3 - - + -
49G VAL* 3.6 15.3 - - + +
53G ALA* 3.6 19.5 - - + -
110H GLU 3.0 19.2 + - - +
111H GLY 3.0 4.4 + - - +
113H LYS* 1.3 77.0 - - - +
115H VAL* 1.3 59.0 + - - +
117H LYS* 3.5 0.6 + - - -
118H TYR* 2.9 30.1 + - - +
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Residues in contact with VAL 115 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY* 3.8 33.9 - - - +
49G VAL* 4.0 8.1 - - + -
50G TYR* 3.9 24.9 - - + +
88H SER* 4.5 9.4 - - - +
111H GLY 3.1 16.5 + - - +
112H THR* 4.0 4.5 - - - +
114H ALA* 1.3 73.5 - - - +
116H THR* 1.3 61.4 + - - +
118H TYR* 3.7 3.4 - - + +
119H THR* 2.9 46.9 + - - +
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Residues in contact with THR 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112H THR* 3.0 23.1 + - - -
113H LYS* 3.7 7.4 - - - +
115H VAL* 1.3 79.9 - - - +
117H LYS* 1.3 62.7 + - - +
119H THR* 3.7 5.0 + - - -
120H SER* 3.4 17.8 + - - -
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Residues in contact with LYS 117 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G SER 4.6 3.4 - - - -
20G ARG* 3.2 21.7 - - - +
21G ALA 3.7 13.7 - - - +
22G GLY* 4.0 16.2 - - - +
113H LYS* 3.2 22.5 + - + +
114H ALA 3.9 3.1 - - - +
116H THR* 1.3 78.8 - - - +
118H TYR* 1.3 64.9 + - - +
120H SER* 3.0 26.2 + - - -
121H ALA* 3.8 1.6 + - - +
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Residues in contact with TYR 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G ARG* 3.3 62.9 + - + +
20G ARG* 3.6 30.3 + - + -
21G ALA* 4.0 7.6 - - + -
45G ALA* 4.2 23.4 + - + +
46G GLY* 5.3 2.9 - - - -
49G VAL* 3.8 25.8 - - + -
114H ALA 2.9 19.7 + - - +
115H VAL* 3.7 4.9 - - + +
117H LYS* 1.3 76.7 - - - +
119H THR* 1.3 71.4 + - - +
121H ALA* 3.0 21.1 + - - +
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Residues in contact with THR 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H VAL* 2.9 30.6 + - - +
116H THR* 4.1 5.2 - - - -
118H TYR* 1.3 79.6 - - - +
120H SER* 1.3 57.4 + - - +
121H ALA 2.9 19.1 + - - +
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Residues in contact with SER 120 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116H THR 3.4 12.3 + - - -
117H LYS* 3.0 18.7 + - - -
119H THR* 1.3 77.3 - - - +
121H ALA* 1.3 57.3 + - - +
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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