Contacts of the helix formed by residues 107 - 122 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105D SER* 2.8 27.7 + - - -
106D LEU* 1.3 79.8 - - - +
108D GLY* 1.3 61.6 + - - +
111D ALA* 3.3 5.2 + - - +
254D GLN 4.4 0.2 - - - -
255D SER* 3.5 4.9 + - - -
257D ALA* 3.9 6.9 - - - +
266D ARG* 3.4 36.7 + - - -
267D VAL 3.3 14.0 + - - -
268D GLY* 3.5 20.4 - - - +
908D PLP 2.5 20.3 + - - -
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Residues in contact with GLY 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D SER* 1.3 71.8 + - - +
109D THR* 1.3 59.1 + - - -
111D ALA* 3.2 5.6 + - - +
112D LEU* 2.8 35.5 + - - +
222D ASP* 5.6 0.2 - - - -
253D CYS 4.9 2.9 - - - -
254D GLN 4.3 5.4 - - - -
255D SER* 3.6 18.6 - - - -
908D PLP 2.6 28.5 + - - -
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Residues in contact with THR 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ARG 3.8 13.2 - - - +
294C GLU 3.8 13.5 - - - +
295C VAL 4.1 3.1 - - - -
296C SER* 3.5 26.1 - - - +
107D SER 3.4 0.2 - - - -
108D GLY* 1.3 76.1 - - - +
110D GLY* 1.3 61.7 + - - +
112D LEU* 3.3 8.0 + - - +
113D HIS* 3.0 21.5 + - - +
140D TRP* 3.3 20.9 - - - -
142D ASN* 3.9 9.2 - - - +
146D ILE* 3.9 12.1 - - + +
266D ARG* 4.2 0.2 - - - -
908D PLP 2.5 26.1 + - - -
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Residues in contact with GLY 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C GLU 3.7 11.9 + - - -
295C VAL* 5.0 0.2 - - - +
105D SER* 4.0 6.3 - - - -
106D LEU* 2.9 34.5 + - - -
107D SER 3.8 0.4 - - - -
109D THR* 1.3 76.4 - - - +
111D ALA* 1.3 58.2 + - - +
113D HIS* 3.1 3.4 + - - +
114D ILE* 2.8 34.6 + - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D SER* 3.5 22.4 - - - +
107D SER 3.3 6.2 + - - +
108D GLY* 3.2 10.4 + - - +
110D GLY* 1.3 76.4 - - - +
112D LEU* 1.3 60.2 + - - +
114D ILE* 3.6 2.2 + - - -
115D SER* 3.2 23.2 + - - -
253D CYS* 3.5 30.1 - - + -
254D GLN 5.0 0.2 - - - +
269D PHE* 3.5 25.5 - - + +
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Residues in contact with LEU 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108D GLY 2.8 33.2 + - - +
109D THR* 3.6 7.6 - - - +
110D GLY 3.2 0.2 - - - -
111D ALA* 1.3 76.8 - - - +
113D HIS* 1.3 58.0 + - - +
115D SER* 3.5 4.4 - - - -
116D ALA* 3.0 27.2 + - - +
143D HIS* 4.3 18.6 - - + +
146D ILE* 3.6 27.5 - - + +
147D PHE* 3.8 27.6 - - + -
187D VAL* 4.8 0.7 - - + -
220D LEU* 3.9 23.8 - - + -
222D ASP* 4.1 17.5 - - - +
253D CYS* 3.5 18.6 - - + -
908D PLP 4.5 4.5 - - + -
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Residues in contact with HIS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C SER 4.4 2.9 - - - -
294C GLU* 3.4 58.1 + - + +
295C VAL* 6.1 0.4 - - - +
109D THR 3.0 8.4 + - - +
110D GLY* 3.1 4.1 + - - +
112D LEU* 1.3 75.6 - - - +
114D ILE* 1.3 69.0 + - - +
115D SER 3.1 1.3 - - - -
116D ALA* 4.4 0.9 - - - +
117D LYS* 2.9 26.5 + - + +
146D ILE* 3.8 11.4 - - + +
149D ASN* 4.2 2.0 - - - -
150D GLN* 3.0 35.4 + - + -
294D GLU* 2.8 41.4 + - - -
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Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D VAL* 4.6 2.0 - - + -
104D GLN 4.5 0.9 - - - +
105D SER* 3.8 25.8 - - - -
110D GLY* 2.8 22.0 + - - +
111D ALA 3.9 3.8 - - - +
113D HIS* 1.3 80.3 - - - +
115D SER* 1.3 58.2 + - - +
117D LYS* 3.4 5.8 + - - +
118D PHE* 3.0 28.6 + - - +
269D PHE* 4.4 20.9 - - + +
287D LEU* 3.8 31.4 - - + +
290D ILE* 4.4 18.8 - - + +
291D ILE* 4.2 28.0 - - + -
294D GLU* 5.9 0.7 - - - +
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Residues in contact with SER 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D ALA 3.2 16.4 + - - -
112D LEU* 3.5 7.2 - - - -
114D ILE* 1.3 79.8 - - - +
116D ALA* 1.3 56.6 + - - +
118D PHE* 3.3 7.6 + - - +
119D PHE* 3.0 54.7 + - - -
147D PHE* 5.3 0.4 - - - -
220D LEU* 3.4 18.9 - - - +
251D PHE* 3.7 10.0 - - - -
253D CYS* 4.6 1.6 - - - -
269D PHE* 3.7 17.5 - - - +
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D LEU 3.0 14.9 + - - +
113D HIS* 3.9 3.8 - - - +
115D SER* 1.3 71.9 - - - +
117D LYS* 1.3 56.6 + - - +
119D PHE* 3.3 1.7 + - - -
120D SER* 2.7 36.4 + - - -
146D ILE* 4.1 11.0 - - + +
147D PHE* 3.5 29.1 - - + -
150D GLN* 3.9 15.5 - - + -
152D LEU* 3.5 16.2 - - + +
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Residues in contact with LYS 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ASN* 2.9 50.4 + - - +
150C GLN* 4.2 7.1 + - - +
113D HIS* 2.9 21.4 + - + +
114D ILE 3.7 4.5 - - - +
116D ALA* 1.3 77.7 - - - +
118D PHE* 1.3 58.2 + - - +
120D SER* 3.3 11.0 + - - +
121D LYS* 2.9 47.6 + - - +
150D GLN* 3.4 27.1 + - - +
290D ILE* 3.9 28.5 - - + -
294D GLU* 4.2 7.0 - - - +
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Residues in contact with PHE 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C PHE* 3.3 43.5 - + - -
9C ILE* 4.8 7.0 - - + -
114D ILE 3.0 17.4 + - - +
115D SER* 3.4 6.7 - - - +
117D LYS* 1.3 76.6 - - - +
119D PHE* 1.3 64.1 + + - +
121D LYS* 4.6 0.9 - - - -
122D PHE* 3.1 65.4 + + - +
123D PHE* 4.1 9.0 - + - -
251D PHE* 4.2 20.0 - + + -
269D PHE* 5.2 3.1 - - - -
283D VAL* 4.2 22.4 - - + -
286D GLN* 4.7 9.4 - - + -
287D LEU* 4.1 19.5 - - + -
290D ILE* 4.2 12.1 - - + +
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Residues in contact with PHE 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5C LEU* 5.6 0.7 - - + -
115D SER* 3.0 40.6 + - - +
116D ALA* 3.7 7.9 - - - +
118D PHE* 1.3 79.5 - + - +
120D SER* 1.3 57.9 + - - +
123D PHE* 2.9 60.3 + + - +
129D PRO* 3.1 0.5 - - - +
131D LYS* 4.8 4.0 - - + -
133D VAL* 5.4 0.9 - - + -
147D PHE* 5.2 3.4 - + - -
152D LEU* 3.8 18.2 - - + -
185D ILE* 3.6 51.8 - - + -
218D ILE* 4.3 6.5 - - + -
220D LEU* 4.1 5.6 - - + -
251D PHE* 3.5 41.5 - + - -
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D ALA 2.7 18.6 + - - -
117D LYS* 3.3 14.2 + - - +
119D PHE* 1.3 79.5 - - - +
121D LYS* 1.3 59.2 + - - +
129D PRO* 3.8 18.1 - - - +
150D GLN* 3.3 37.4 + - - -
152D LEU* 4.0 10.5 - - - -
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Residues in contact with LYS 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ASN* 3.7 14.4 + - - +
117D LYS* 2.9 34.8 + - - +
118D PHE* 4.0 4.0 - - - +
119D PHE 3.3 0.2 - - - -
120D SER* 1.3 80.2 - - - +
122D PHE* 1.3 89.8 + - + +
129D PRO* 4.6 2.9 - - - +
286D GLN* 4.8 6.7 + - - +
289D LYS* 5.4 7.1 - - - +
290D ILE* 3.5 29.5 - - + +
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Residues in contact with PHE 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C ILE* 3.6 22.9 - - + -
10C GLU 6.0 0.4 - - - -
118D PHE* 3.1 57.4 + + - -
121D LYS* 1.3 103.8 - - + +
123D PHE* 1.3 91.7 + - + +
129D PRO* 3.5 8.0 - - - +
286D GLN* 3.4 37.5 - - + -
290D ILE* 5.6 1.8 - - + -
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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