Contacts of the helix formed by residues 106 - 117 (chain B) in PDB entry 1YI8
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 PRO 106 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B SER 4.4 4.9 - - - +
104B ALA* 3.4 10.8 - - - +
105B VAL* 1.3 84.6 - - - +
107B GLU* 1.3 76.1 + - - +
108B LEU 3.0 0.2 - - - -
109B ALA* 2.9 22.7 + - + +
110B GLU* 3.1 11.2 + - - +
332B ARG* 3.5 22.2 - - - +
106C PRO* 5.5 8.7 - - + +
110C GLU* 4.2 32.6 + - + +
343C ARG* 5.5 2.7 - - - +
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Residues in contact with GLU 107 (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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105B VAL* 3.0 3.1 + - + +
106B PRO* 1.3 83.2 - - - +
108B LEU* 1.3 57.2 + - - +
110B GLU* 3.3 17.5 + - - +
111B LEU* 3.0 28.4 + - - +
332B ARG* 2.7 52.7 + - - +
335B ALA* 3.9 16.8 - - + -
336B ALA* 4.1 26.3 - - - +
339B LEU* 3.7 26.5 - - + +
343B ARG* 5.0 4.3 + - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B LEU* 4.5 1.8 - - + -
102B GLN* 3.7 26.9 - - + +
105B VAL* 2.9 37.2 + - + +
107B GLU* 1.3 75.2 - - - +
109B ALA* 1.3 54.9 + - - +
111B LEU* 3.5 4.6 + - - +
112B THR* 2.6 37.3 + - - +
153B SER 6.0 0.2 - - - +
156B ALA* 3.8 8.1 - - + +
157B ASP* 3.3 28.5 - - - +
160B ALA* 3.5 30.3 - - + -
161B PHE* 3.9 26.2 - - + -
335B ALA* 4.3 1.6 - - + -
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Residues in contact with ALA 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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63B VAL* 6.5 0.2 - - + -
105B VAL 4.3 0.2 + - - -
106B PRO* 2.9 12.6 + - + +
108B LEU* 1.3 76.6 - - - +
110B GLU* 1.3 67.6 + - - +
112B THR* 3.2 9.0 + - - -
113B VAL* 3.1 27.4 + - - +
109C ALA* 4.3 1.6 - - - -
110C GLU* 3.7 19.3 - - + +
113C VAL* 3.5 33.4 - - + +
114C TYR* 6.1 0.4 - - + -
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Residues in contact with GLU 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 PRO 3.1 10.1 + - - +
107B GLU* 3.4 15.4 - - - +
109B ALA* 1.3 79.2 - - - +
111B LEU* 1.3 62.4 + - - +
113B VAL* 3.3 12.0 + - - +
114B TYR* 3.4 41.0 + - + +
339B LEU* 3.6 11.3 - - + +
343B ARG* 2.8 49.2 + - - +
103C SER 4.9 3.1 - - - +
106C PRO* 3.7 30.0 - - + +
109C ALA* 3.7 17.6 - - + +
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU 3.0 16.1 + - - +
108B LEU* 3.9 5.2 - - - +
110B GLU* 1.3 74.0 - - - +
112B THR* 1.3 66.0 + - - +
114B TYR* 3.4 9.5 + - + -
115B PHE* 3.0 49.2 + - + +
156B ALA* 3.5 31.4 - - + +
159B ALA* 4.0 10.1 - - + -
160B ALA* 3.7 22.4 - - + +
186B PHE* 5.1 0.4 - - + -
194B LEU* 5.6 0.2 - - + -
338B THR* 5.5 1.1 - - + -
339B LEU* 4.2 11.4 - - + +
342B VAL* 4.1 33.9 - - + -
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Residues in contact with THR 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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108B LEU* 2.6 23.1 + - - +
109B ALA* 3.2 11.6 + - - -
111B LEU* 1.3 75.8 - - - +
113B VAL* 1.3 65.4 + - + +
115B PHE* 3.1 6.1 + - - +
116B LEU* 2.9 30.6 + - + +
149B VAL* 5.0 5.2 - - + -
152B VAL* 3.8 21.1 - - + -
153B SER* 3.8 23.1 + - - -
156B ALA* 3.5 15.4 - - - +
113C VAL* 5.8 11.0 - - + +
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Residues in contact with VAL 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 ALA 3.1 14.0 + - - +
110B GLU 3.5 7.4 - - - +
112B THR* 1.3 78.2 - - + +
114B TYR* 1.3 67.9 + - + +
116B LEU* 3.1 30.7 + - + +
117B ASN* 3.8 10.5 + - - +
63C VAL* 4.0 27.6 - - + -
109C ALA* 3.8 21.3 - - + +
112C THR* 3.8 23.6 - - + +
113C VAL* 5.6 2.0 - - + +
146C GLY* 5.3 0.2 - - - -
153C SER* 6.0 5.4 - - - -
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Residues in contact with TYR 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 GLU* 3.4 48.2 + - + +
111B LEU* 3.8 17.3 - - + +
112B THR 3.3 0.8 - - - -
113B VAL* 1.3 81.2 - - + +
115B PHE* 1.3 65.0 + - + +
117B ASN* 3.2 26.0 + - - +
118B LEU* 4.0 8.2 - - - +
186B PHE* 5.3 2.2 - - + -
190B TYR* 5.4 2.4 + - + -
339B LEU* 4.5 5.8 - - + -
342B VAL* 4.2 8.1 - - + -
343B ARG* 4.7 0.7 - - + -
346B MET* 3.3 45.8 - - + -
348B LEU* 3.3 24.3 - - + +
63C VAL* 4.6 24.5 - - + +
66C LEU* 5.0 8.5 - - + -
103C SER* 4.4 10.6 + - - -
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Residues in contact with PHE 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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111B LEU* 3.0 34.6 + - + +
112B THR 3.1 8.7 + - - +
114B TYR* 1.3 76.2 - - + +
116B LEU* 1.3 60.6 + - - +
118B LEU* 2.8 36.4 + - + +
119B VAL* 4.0 4.3 + - - +
152B VAL* 4.3 13.5 - - + -
155B ALA* 3.6 32.8 - - + -
156B ALA* 3.8 20.4 - - + -
159B ALA* 3.6 20.9 - - + -
182B ILE* 3.6 31.1 - - + +
183B VAL* 4.8 5.2 - - + -
186B PHE* 3.9 20.9 - + - -
194B LEU* 3.8 11.4 - - + -
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Residues in contact with LEU 116 (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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112B THR* 2.9 24.6 + - + +
113B VAL* 3.1 22.2 + - + +
115B PHE* 1.3 75.9 - - - +
117B ASN* 1.3 60.6 + - - +
118B LEU 3.1 1.1 + - - -
119B VAL* 3.4 4.9 + - - +
149B VAL* 3.9 22.4 - - + -
152B VAL* 3.6 26.2 - - + -
116C LEU* 4.6 18.2 - - + -
145C ALA* 3.0 31.5 + - + +
146C GLY* 2.9 28.4 + - - +
149C VAL* 4.3 21.5 - - + -
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Residues in contact with ASN 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 VAL* 4.1 11.2 + - - +
114B TYR* 3.2 19.9 + - - +
115B PHE 3.0 0.8 + - - -
116B LEU* 1.3 77.0 - - - +
118B LEU* 1.3 60.9 + - + +
119B VAL 3.5 2.0 + - - -
190B TYR* 5.4 1.2 + - - +
63C VAL* 4.7 2.8 - - - +
66C LEU* 3.3 29.0 - - - +
67C THR* 3.3 24.7 + - - +
70C PHE* 3.7 47.7 - - + +
144C PRO* 4.1 8.5 - - - +
146C GLY* 3.3 19.8 - - - +
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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
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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