Contacts of the helix formed by residues 105 - 122 (chain H) in PDB entry 4KYI
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 ASN 105 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102H ASP* 2.9 14.1 + - + +
103H ILE 3.0 3.6 + - - -
104H THR* 1.3 82.3 + - - +
106H THR* 1.3 60.9 + - - +
107H ASP* 3.1 28.8 + - - +
108H THR* 2.7 48.4 + - + +
109H PHE* 3.5 5.9 + - - +
143H ALA* 4.3 1.9 - - - +
144H VAL* 4.1 3.4 - - - +
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Residues in contact with THR 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105H ASN* 1.3 73.5 + - - +
107H ASP* 1.3 56.1 + - - +
109H PHE* 3.1 13.8 + - + +
110H ALA* 2.8 33.4 + - + +
143H ALA* 3.7 24.4 + - - +
144H VAL* 3.8 15.7 - - + +
148H GLU* 5.1 7.0 - - - +
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Residues in contact with ASP 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 6.0 0.7 - - - -
105H ASN* 3.1 14.1 + - - +
106H THR* 1.3 77.5 - - - +
108H THR* 1.3 56.3 + - + +
110H ALA* 2.9 10.9 + - - +
111H ARG* 2.6 37.6 + - - +
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Residues in contact with THR 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 4.0 26.8 + - + +
30H SER 5.2 1.6 - - - +
32H VAL* 4.1 15.5 - - + -
100H VAL 4.7 1.7 - - - +
101H TYR* 3.4 5.7 - - - +
102H ASP* 2.8 30.8 + - + -
105H ASN* 2.7 43.7 + - + +
107H ASP* 1.3 77.2 - - + +
109H PHE* 1.3 56.0 + - - +
111H ARG* 3.9 7.7 - - - +
112H ALA* 3.0 26.3 + - - +
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Residues in contact with PHE 109 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H TYR* 3.8 41.3 - + + -
105H ASN 3.9 3.4 - - - +
106H THR* 3.1 19.7 + - + +
107H ASP 3.1 0.2 - - - -
108H THR* 1.3 79.5 + - - +
110H ALA* 1.3 64.1 + - + +
112H ALA* 3.3 14.9 + - + +
113H LYS* 3.5 44.5 + - + +
131H LEU* 4.7 8.3 - - + -
144H VAL* 4.0 16.2 - - + -
148H GLU* 3.8 29.4 - - + -
149H ALA* 3.5 39.9 - - + -
152H TYR* 4.9 5.6 - + + -
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Residues in contact with ALA 110 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H THR* 2.8 15.0 + - + +
107H ASP* 2.9 14.3 + - - +
109H PHE* 1.3 78.9 - - + +
111H ARG* 1.3 64.1 + - - +
112H ALA 3.1 0.2 - - - -
113H LYS* 3.2 26.2 + - + +
114H ASN* 3.5 12.9 + - - +
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Residues in contact with ARG 111 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H GLU* 3.6 33.6 + - + +
79H GLY 5.1 4.0 + - - -
80H LEU 5.7 0.2 + - - -
81H GLU* 4.2 21.0 + - - +
84H HIS* 4.2 22.2 + - - +
107H ASP 2.6 19.2 + - - +
108H THR* 3.9 8.3 - - - +
110H ALA* 1.3 69.8 - - - +
112H ALA* 1.3 65.0 + - - +
114H ASN* 3.2 34.4 + - - +
115H TRP* 3.1 84.1 + - + +
118H GLU* 5.2 3.2 + - - -
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Residues in contact with ALA 112 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H GLY* 5.9 0.7 - - - -
29H GLU 6.0 0.2 - - - +
99H VAL* 3.5 23.6 - - + +
100H VAL 4.7 2.2 - - - +
101H TYR* 4.0 16.2 - - + -
108H THR 3.0 19.9 + - - +
109H PHE* 3.3 11.4 - - + +
110H ALA 3.1 0.2 - - - -
111H ARG* 1.3 78.0 - - - +
113H LYS* 1.3 62.0 + - + +
115H TRP* 3.2 4.4 + - - -
116H VAL* 3.0 27.0 + - - +
131H LEU* 4.1 12.3 - - + -
152H TYR* 5.7 0.7 - - + -
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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
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109H PHE* 3.5 47.3 - - + +
110H ALA* 3.2 12.3 + - - +
112H ALA* 1.3 78.2 - - + +
114H ASN* 1.3 54.6 + - - +
116H VAL* 3.1 3.1 + - - +
117H LYS* 2.6 37.4 + - - +
148H GLU* 5.6 1.2 + - - +
152H TYR* 3.4 48.4 + - + +
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Residues in contact with ASN 114 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H ALA 3.5 14.0 + - - +
111H ARG* 3.2 35.5 + - - +
113H LYS* 1.3 79.8 - - - +
115H TRP* 1.3 57.3 + - - +
117H LYS* 3.2 23.3 + - + +
118H GLU* 2.8 30.9 + - - +
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Residues in contact with TRP 115 (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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27H LEU* 3.9 43.5 - - + -
28H GLY* 4.1 29.0 - - - -
29H GLU* 5.1 0.4 - - - +
78H ALA 5.6 1.1 - - - -
79H GLY* 4.8 13.0 + - - -
80H LEU 5.8 0.9 - - - -
83H TYR 5.7 0.4 - - - -
84H HIS* 3.9 23.3 - + + -
87H ALA* 3.9 21.8 - - + -
91H TYR* 5.2 2.0 - + - -
99H VAL* 3.9 12.6 - - + -
111H ARG* 3.1 68.2 + - + +
112H ALA* 3.5 7.9 - - - +
113H LYS 3.2 0.2 - - - -
114H ASN* 1.3 75.2 - - - +
116H VAL* 1.3 59.4 + - - +
118H GLU* 3.3 22.1 + - + +
119H LEU* 2.8 35.8 + - + +
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Residues in contact with VAL 116 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99H VAL* 3.9 21.8 - - + -
112H ALA 3.0 17.5 + - - +
113H LYS 3.4 0.7 - - - +
115H TRP* 1.3 71.7 - - - +
117H LYS* 1.3 55.7 + - - +
119H LEU* 3.0 8.6 + - - +
120H GLN* 2.6 60.2 + - + +
129H ILE* 4.4 4.7 - - + -
131H LEU* 4.5 3.8 - - + -
152H TYR* 3.4 27.1 - - + +
156H ASN* 4.5 4.5 - - - +
158H LEU* 3.8 31.2 - - + -
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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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113H LYS 2.6 21.0 + - - +
114H ASN* 3.2 24.5 + - - +
116H VAL* 1.3 72.4 - - - +
118H GLU* 1.3 61.4 + - - +
120H GLN* 3.2 18.5 + - - +
121H ARG* 3.3 55.0 + - - +
152H TYR* 4.9 0.2 + - - -
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Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H HIS* 3.1 36.5 - - - +
87H ALA* 5.2 0.5 - - - +
88H PRO* 5.3 2.9 - - - +
91H TYR* 3.5 28.3 + - + +
111H ARG* 5.2 2.1 + - - -
114H ASN 2.8 20.5 + - - +
115H TRP* 3.6 23.2 - - + +
117H LYS* 1.3 74.1 - - - +
119H LEU* 1.3 62.0 + - + +
121H ARG* 4.5 9.9 - - - +
122H GLN* 3.3 45.5 + - - +
123H ALA* 3.9 2.5 + - - +
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Residues in contact with LEU 119 (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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27H LEU* 3.7 31.4 - - + -
91H TYR* 4.0 30.1 - - + -
97H ALA* 4.0 14.4 - - + -
99H VAL* 3.7 24.0 - - + -
115H TRP* 2.8 24.4 + - + +
116H VAL 3.5 3.8 - - - +
118H GLU* 1.3 75.0 - - + +
120H GLN* 1.3 65.5 + - - +
123H ALA* 3.2 30.3 + - + +
124H SER 4.8 1.0 - - - +
127H ILE* 4.3 16.0 - - + +
129H ILE* 3.7 24.2 - - + +
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Residues in contact with GLN 120 (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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116H VAL* 2.6 36.3 + - + +
117H LYS* 3.5 10.1 - - - +
118H GLU 3.2 0.4 - - - -
119H LEU* 1.3 75.3 - - - +
121H ARG* 1.3 60.5 + - + +
123H ALA 5.2 0.9 - - - +
125H PRO* 5.6 5.4 - - - +
129H ILE* 3.9 18.1 - - + +
156H ASN* 3.5 41.0 + - - +
158H LEU* 4.1 2.6 - - - +
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Residues in contact with ARG 121 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H LYS* 3.3 64.9 + - - +
118H GLU* 4.0 7.5 - - - +
119H LEU 3.3 0.2 - - - -
120H GLN* 1.3 79.7 - - + +
122H GLN* 1.3 76.2 + - + +
123H ALA 3.1 18.3 + - - +
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Residues in contact with GLN 122 (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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88H PRO* 5.5 4.2 - - - +
91H TYR* 3.5 24.5 + - - +
118H GLU* 3.3 38.1 + - + +
121H ARG* 1.3 91.1 + - + +
123H ALA* 1.3 57.2 + - - +
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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
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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