Contacts of the helix formed by residues 105 - 123 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102B ASP* 2.8 19.5 + - + +
103B ILE 3.2 1.8 - - - -
104B THR* 1.3 83.0 + - - +
106B THR* 1.3 61.1 + - - +
107B ASP* 2.9 28.2 + - - +
108B THR* 2.5 50.3 + - + +
109B PHE 3.6 1.6 + - - -
143B ALA* 4.6 0.7 - - - -
144B VAL* 3.9 1.9 - - - +
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 1.3 72.7 + - - +
107B ASP* 1.3 62.1 + - - +
109B PHE* 3.2 12.7 + - + +
110B ALA* 2.9 26.3 + - + +
143B ALA* 3.7 26.5 + - - +
144B VAL* 4.1 13.9 - - + -
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Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 2.9 13.4 + - - +
106B THR* 1.3 82.0 - - - +
108B THR* 1.3 54.5 + - - +
110B ALA* 3.1 11.5 + - - +
111B ARG* 2.8 34.7 + - - +
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Residues in contact with THR 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 4.2 21.7 + - + +
30B SER 5.2 2.2 - - - +
31B ALA 5.9 0.2 - - - +
32B VAL* 4.0 17.3 - - + -
100B VAL 5.1 0.7 - - - +
101B TYR* 3.5 9.1 - - - +
102B ASP* 2.9 35.6 + - + +
105B ASN* 2.5 46.5 + - + +
107B ASP* 1.3 76.4 - - - +
109B PHE* 1.3 55.2 + - - +
111B ARG* 3.3 8.1 + - - +
112B ALA* 3.0 22.3 + - - +
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Residues in contact with PHE 109 (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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101B TYR* 3.5 50.7 - + + -
106B THR* 3.2 15.4 + - + +
108B THR* 1.3 81.2 + - - +
110B ALA* 1.3 64.1 + - - +
112B ALA* 3.3 11.3 + - + +
113B LYS* 3.3 42.8 + - + +
131B LEU* 4.5 6.1 - - + -
144B VAL* 3.6 28.9 - - + -
148B GLU* 4.2 17.9 - - + -
149B ALA* 4.1 24.9 - - + -
152B TYR* 4.4 21.8 - + + -
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Residues in contact with ALA 110 (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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106B THR* 2.9 16.7 + - + +
107B ASP* 3.1 17.7 + - + +
109B PHE* 1.3 77.1 - - + +
111B ARG* 1.3 61.1 + - - +
113B LYS* 3.5 29.6 - - + +
114B ASN* 3.9 11.1 + - - +
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Residues in contact with ARG 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B GLU* 3.6 29.8 + - + +
81B GLU* 4.1 19.8 + - - +
84B HIS* 3.7 21.2 + - - +
107B ASP 2.8 14.9 + - - +
108B THR* 3.5 9.4 - - - +
110B ALA* 1.3 74.3 - - - +
112B ALA* 1.3 59.9 + - - +
113B LYS 3.1 2.2 - - - -
114B ASN* 2.9 56.1 + - - +
115B TRP* 3.2 59.8 + - + +
118B GLU* 4.9 2.6 + - - -
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Residues in contact with ALA 112 (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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28B GLY* 6.0 1.1 - - - -
99B VAL* 3.6 24.6 - - + +
100B VAL 5.1 1.3 - - - +
101B TYR* 4.1 15.3 - - + +
108B THR 3.0 13.8 + - - +
109B PHE* 3.3 13.9 + - + +
111B ARG* 1.3 77.4 - - - +
113B LYS* 1.3 60.7 + - - +
115B TRP* 3.3 5.9 + - - +
116B VAL* 3.1 30.4 + - - +
131B LEU* 4.5 12.8 - - + -
152B TYR* 5.6 0.7 - - + -
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Residues in contact with LYS 113 (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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109B PHE* 3.4 48.3 - - + +
110B ALA* 3.5 17.9 - - + +
111B ARG 3.1 0.6 - - - -
112B ALA* 1.3 78.8 - - + +
114B ASN* 1.3 58.8 + - - +
116B VAL* 3.9 0.4 - - - +
117B LYS* 3.1 29.1 + - - +
148B GLU* 4.6 8.3 + - - +
152B TYR* 3.4 49.4 + - + +
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Residues in contact with ASN 114 (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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110B ALA 4.1 12.9 + - - +
111B ARG* 2.9 34.8 + - - +
113B LYS* 1.3 80.1 - - - +
115B TRP* 1.3 59.9 - - - +
117B LYS* 3.5 8.9 + - - +
118B GLU* 2.8 31.1 + - - +
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Residues in contact with TRP 115 (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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27B LEU* 4.1 33.0 - - + -
28B GLY* 3.8 36.7 - - - +
29B GLU* 5.2 0.2 - - - +
79B GLY* 5.5 6.9 + - - -
80B LEU 6.0 1.6 - - - -
83B TYR 5.6 0.2 - - - -
84B HIS* 3.4 26.7 - + + -
87B ALA* 3.9 24.0 - - + -
91B TYR* 5.1 2.5 - + - -
99B VAL* 3.9 14.1 - - + -
111B ARG* 3.2 58.9 + - + +
112B ALA* 3.3 8.9 + - - +
114B ASN* 1.3 73.7 - - - +
116B VAL* 1.3 55.1 + - - +
118B GLU* 3.1 31.0 + - - +
119B LEU* 2.6 41.9 + - + +
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Residues in contact with VAL 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B VAL* 3.9 21.1 - - + -
112B ALA 3.1 17.4 + - - +
113B LYS* 3.9 5.2 - - - +
115B TRP* 1.3 75.7 - - - +
117B LYS* 1.3 55.0 + - - +
119B LEU* 3.0 10.2 + - - +
120B GLN* 2.8 59.0 + - + +
129B ILE* 4.5 6.3 - - + -
130B ALA 5.6 0.2 - - - +
131B LEU* 5.3 3.1 - - + -
152B TYR* 4.3 13.2 - - + +
156B ASN* 4.9 4.7 - - + +
158B LEU* 4.0 39.3 - - + -
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Residues in contact with LYS 117 (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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113B LYS 3.1 17.0 + - - +
114B ASN* 3.9 9.0 - - - +
116B VAL* 1.3 79.8 - - - +
118B GLU* 1.3 59.3 + - - +
120B GLN* 3.9 15.7 - - + +
121B ARG* 3.2 43.7 + - + +
152B TYR* 5.4 1.8 - - - +
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Residues in contact with GLU 118 (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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84B HIS* 3.2 34.9 - - - +
87B ALA* 4.8 3.3 - - - +
88B PRO* 5.4 2.8 - - - +
91B TYR* 3.8 21.4 + - + +
111B ARG* 4.9 2.4 + - - -
114B ASN 2.8 17.9 + - - +
115B TRP* 3.3 26.9 - - + +
117B LYS* 1.3 76.3 - - - +
119B LEU* 1.3 59.4 + - - +
121B ARG* 3.4 5.4 + - + +
122B GLN* 3.0 33.7 + - + +
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Residues in contact with LEU 119 (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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27B LEU* 4.0 18.2 - - + -
91B TYR* 4.0 26.5 - - + -
97B ALA* 3.7 28.9 - - + -
99B VAL* 3.9 24.7 - - + -
115B TRP* 2.6 24.7 + - + +
116B VAL* 3.3 5.8 - - - +
118B GLU* 1.3 73.8 - - - +
120B GLN* 1.3 59.8 + - - +
123B ALA* 2.8 52.8 + - + +
124B SER 5.0 1.0 - - - +
127B ILE* 4.4 2.8 - - + +
129B ILE* 3.7 24.0 - - + -
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Residues in contact with GLN 120 (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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116B VAL* 2.8 35.1 + - + +
117B LYS* 3.9 21.2 - - - +
119B LEU* 1.3 72.5 - - - +
121B ARG* 1.3 62.9 + - + +
123B ALA 4.9 3.5 - - - +
125B PRO* 5.9 2.4 - - - +
127B ILE* 6.2 0.9 - - - -
129B ILE* 4.2 12.7 - - + +
156B ASN* 3.9 32.0 + - - +
157B SER* 5.8 0.8 - - - -
158B LEU* 5.4 0.6 - - - +
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Residues in contact with ARG 121 (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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117B LYS* 3.2 33.2 + - + +
118B GLU* 3.4 8.2 + - + +
119B LEU 3.2 0.6 - - - -
120B GLN* 1.3 81.6 - - + +
122B GLN* 1.3 74.7 + - - +
123B ALA 4.7 1.6 - - - +
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Residues in contact with GLN 122 (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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88B PRO* 5.7 5.6 - - + -
91B TYR* 3.4 28.2 - - + +
118B GLU* 3.0 14.6 + - + +
121B ARG* 1.3 90.2 - - - +
123B ALA* 1.3 69.8 + - - +
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Residues in contact with ALA 123 (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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91B TYR* 3.7 29.9 - - + +
92B ARG* 6.0 0.9 - - - +
119B LEU* 2.8 39.7 + - + +
120B GLN 4.9 2.9 - - - +
121B ARG 4.7 2.4 - - - +
122B GLN* 1.3 79.9 + - - +
124B SER* 1.3 71.7 + - - +
125B PRO* 3.6 4.0 - - - +
127B ILE* 4.3 12.6 - - + -
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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