Contacts of the helix formed by residues 107 - 122 (chain C) in PDB entry 1YAA
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 SER 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C SER* 2.7 32.3 + - - -
106C LEU* 1.3 75.5 - - - +
108C GLY* 1.3 60.8 + - - -
111C ALA* 3.2 6.9 + - - +
254C GLN 4.0 0.6 - - - +
255C SER* 3.8 3.1 + - - -
257C ALA* 3.9 6.2 - - - +
266C ARG* 3.4 28.8 + - - -
267C VAL 3.4 15.8 + - - -
268C GLY* 3.5 20.9 - - - +
907C PLP 2.5 26.4 + - - -
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C SER* 1.3 70.7 + - - +
109C THR* 1.3 60.6 + - - +
110C GLY 3.2 0.2 - - - -
111C ALA* 3.4 5.4 + - - +
112C LEU* 2.8 35.2 + - - +
222C ASP* 5.5 0.4 - - - -
253C CYS* 4.2 4.6 - - - +
254C GLN 4.0 12.8 - - - -
255C SER* 3.9 7.5 - - - -
907C PLP 2.8 31.5 + - - -
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Residues in contact with THR 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLY* 1.3 75.4 - - - +
110C GLY* 1.3 57.4 + - - +
112C LEU* 3.3 10.2 + - - +
113C HIS* 2.8 27.5 + - - +
140C TRP* 3.5 16.8 - - - -
142C ASN* 4.3 1.1 - - - +
146C ILE* 3.9 17.2 - - + +
907C PLP 2.7 23.3 + - - -
292D ARG 3.8 12.6 - - - +
293D SER 4.5 1.1 - - - +
294D GLU 3.7 9.9 - - - +
295D VAL 4.1 3.8 - - - -
296D SER* 3.3 36.6 + - - +
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Residues in contact with GLY 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C SER* 3.8 6.5 - - - -
106C LEU* 3.0 33.7 + - - -
107C SER 3.9 0.9 - - - -
108C GLY 3.2 0.2 - - - -
109C THR* 1.3 75.5 - - - +
111C ALA* 1.3 58.5 + - - +
113C HIS* 3.0 4.5 + - - +
114C ILE* 2.9 34.0 + - - +
294D GLU 3.8 11.2 + - - -
295D VAL* 5.5 0.2 - - - -
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Residues in contact with ALA 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C SER* 3.3 21.1 + - - +
107C SER 3.2 9.1 + - - +
108C GLY* 3.7 8.5 - - - +
110C GLY* 1.3 73.2 - - - +
112C LEU* 1.3 62.1 + - - +
114C ILE* 3.3 2.6 + - - -
115C SER* 3.0 27.4 + - - -
253C CYS* 3.6 20.9 - - + -
269C PHE* 3.5 34.4 - - + +
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Residues in contact with LEU 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C GLY 2.8 18.5 + - - +
109C THR* 3.4 5.8 - - - +
111C ALA* 1.3 77.7 - - - +
113C HIS* 1.3 55.3 + - - +
115C SER* 3.4 4.8 - - - -
116C ALA* 3.2 21.0 + - - +
140C TRP* 3.8 17.0 - - + -
143C HIS* 4.1 12.3 - - + +
146C ILE* 3.8 23.9 - - + +
147C PHE* 4.4 13.6 - - + -
220C LEU* 4.0 16.4 - - + -
222C ASP* 4.0 8.3 - - + +
253C CYS* 3.1 33.8 - - + -
907C PLP 3.5 29.6 - - + +
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Residues in contact with HIS 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C THR 2.8 16.4 + - - +
110C GLY* 3.0 5.4 + - - +
112C LEU* 1.3 73.9 - - - +
114C ILE* 1.3 64.1 + - - +
115C SER 3.1 1.8 - - - -
116C ALA* 3.3 1.4 + - - +
117C LYS* 3.0 30.2 + - + +
146C ILE* 4.0 9.2 - - + +
149C ASN* 4.3 0.2 - - - -
150C GLN* 3.2 34.0 + - + -
290C ILE* 5.7 0.2 - - - +
294C GLU* 2.8 39.8 + - - -
113D HIS* 4.9 0.2 - + - -
293D SER 4.1 6.7 - - - +
294D GLU* 3.4 51.2 + - + +
295D VAL* 6.0 0.6 - - - +
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Residues in contact with ILE 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C VAL* 4.6 2.9 - - + -
104C GLN 4.7 0.2 - - - +
105C SER* 3.8 28.7 - - - -
110C GLY 2.9 14.0 + - - +
111C ALA 3.3 6.5 + - - +
113C HIS* 1.3 80.5 - - - +
115C SER* 1.3 61.8 + - - +
117C LYS* 4.0 5.9 - - - +
118C PHE* 3.1 23.4 + - - +
269C PHE* 4.4 22.0 - - + +
287C LEU* 3.8 32.1 - - + +
290C ILE* 4.8 15.9 - - + +
291C ILE* 4.3 27.6 - - + -
294C GLU* 6.0 0.2 - - - +
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Residues in contact with SER 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ALA 3.0 13.4 + - - -
112C LEU 3.4 10.8 - - - -
113C HIS 3.1 0.2 - - - -
114C ILE* 1.3 76.9 - - - +
116C ALA* 1.3 58.5 + - - +
118C PHE* 3.3 6.2 + - - +
119C PHE* 3.0 42.7 + - - -
147C PHE* 5.0 0.7 - - - -
220C LEU* 4.0 21.1 - - - +
251C PHE* 3.9 7.0 - - - -
253C CYS* 3.7 10.4 - - - -
269C PHE* 3.1 21.8 + - - +
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Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C LEU 3.2 10.9 + - - +
113C HIS* 3.3 7.6 + - - +
115C SER* 1.3 77.5 - - - +
117C LYS* 1.3 59.6 + - - +
119C PHE* 3.3 4.0 + - - +
120C SER* 2.9 30.0 + - - -
146C ILE 3.8 14.6 - - - +
147C PHE* 3.9 17.7 - - + -
150C GLN* 3.4 23.3 - - + +
152C LEU* 3.7 13.2 - - + +
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Residues in contact with LYS 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C HIS* 3.0 20.5 + - - +
114C ILE 4.0 3.6 - - - +
116C ALA* 1.3 76.6 - - - +
118C PHE* 1.3 61.5 + - - +
120C SER* 2.7 21.7 + - - +
121C LYS* 3.0 22.8 + - + +
150C GLN* 3.3 23.1 + - - +
290C ILE* 3.7 33.4 - - + -
294C GLU* 4.1 6.5 - - - +
149D ASN* 2.9 54.5 + - - +
150D GLN* 3.9 10.3 + - - +
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Residues in contact with PHE 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C ILE 3.1 18.3 + - - +
115C SER* 3.4 6.3 - - - +
117C LYS* 1.3 79.7 - - - +
119C PHE* 1.3 63.7 + + - +
121C LYS* 3.3 0.9 + - - -
122C PHE* 3.1 60.2 + + - +
123C PHE* 4.1 8.3 - + - -
251C PHE* 4.2 20.0 - + + -
269C PHE* 5.1 1.3 - + - -
283C VAL* 4.2 23.1 - - + -
286C GLN* 4.3 8.7 - - + -
287C LEU* 3.9 19.1 - - + -
290C ILE* 4.4 12.5 - - + +
6D PHE* 3.5 40.2 - + - -
9D ILE* 3.8 16.6 - - + -
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Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C SER* 3.0 36.7 + - - +
116C ALA* 3.7 7.6 - - - +
117C LYS 3.3 0.2 - - - -
118C PHE* 1.3 78.4 - + - +
120C SER* 1.3 59.3 + - - +
123C PHE* 2.8 64.6 + + + +
129C PRO 2.9 0.3 - - - -
131C LYS* 5.2 1.3 - - + -
133C VAL* 5.3 0.9 - - + -
147C PHE* 5.1 4.3 - + - -
152C LEU* 3.8 20.2 - - + -
185C ILE* 3.7 48.0 - - + -
218C ILE* 4.4 6.3 - - + -
220C LEU* 4.5 7.0 - - + -
251C PHE* 3.5 43.7 - + - -
5D LEU* 5.6 1.8 - - + -
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Residues in contact with SER 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C ALA 2.9 14.1 + - - -
117C LYS* 2.7 30.1 + - - +
119C PHE* 1.3 76.7 - - - +
121C LYS* 1.3 62.1 + - - +
129C PRO* 3.4 21.1 - - - +
150C GLN* 3.3 35.5 + - - -
152C LEU* 3.7 10.9 - - - +
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Residues in contact with LYS 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LYS* 3.0 25.7 + - + +
118C PHE* 3.7 4.5 - - - +
120C SER* 1.3 81.2 + - - +
122C PHE* 1.3 85.1 + - + +
129C PRO* 4.4 2.4 - - - +
286C GLN* 4.0 16.2 + - - +
289C LYS* 4.7 19.4 - - - +
290C ILE* 5.0 17.6 - - + +
12D LEU* 5.3 2.6 - - - +
149D ASN* 5.7 3.0 + - - -
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Residues in contact with PHE 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C PHE* 3.1 57.7 + + - +
121C LYS* 1.3 103.3 - - + +
123C PHE* 1.3 89.1 + - + +
129C PRO* 3.4 9.6 - - - +
130C ASP* 5.0 0.3 - - - +
286C GLN* 3.4 37.0 - - + -
290C ILE* 5.5 0.7 - - + -
9D ILE* 4.1 27.1 - - + -
10D GLU 5.9 0.2 - - - -
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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