Contacts of the helix formed by residues 138 - 150 (chain D) in PDB entry 2YIN
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 THR 138 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ARG* 3.8 9.4 - - - +
136D PRO 4.3 5.4 - - - +
137D ILE* 1.3 79.6 - - - +
139D TYR* 1.3 66.4 + - - +
140D PRO* 3.7 12.1 - - - +
141D GLN* 2.5 48.1 + - - +
142D GLY* 3.0 19.1 + - - -
154D TYR* 4.2 0.7 + - - -
156D GLU* 4.3 0.7 - - - -
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Residues in contact with TYR 139 (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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120D ARG* 3.5 13.7 - - - +
138D THR* 1.3 69.9 - - - +
140D PRO* 1.4 76.5 - - + +
142D GLY 3.2 1.6 + - - -
143D LEU* 3.0 49.8 + - + +
154D TYR* 3.7 28.9 + + - -
155D LEU* 6.0 0.2 - - - -
156D GLU* 3.4 36.3 - - + +
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Residues in contact with PRO 140 (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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138D THR* 3.6 14.1 - - - +
139D TYR* 1.4 101.5 - - + +
141D GLN* 1.3 59.5 + - + +
143D LEU* 3.6 7.1 + - + +
144D ALA* 3.2 23.4 + - - +
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Residues in contact with GLN 141 (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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90D PHE* 3.5 10.2 - - + -
135D THR* 5.3 3.2 + - - -
136D PRO 3.7 6.9 + - - -
137D ILE* 3.4 26.4 - - + +
138D THR* 2.5 51.3 + - - +
140D PRO* 1.3 75.7 - - + +
142D GLY* 1.3 64.8 + - - +
144D ALA* 3.4 6.5 + - - +
145D MET* 3.1 23.6 + - - +
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Residues in contact with GLY 142 (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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90D PHE* 3.8 15.7 - - - -
112D LEU* 3.5 8.3 - - - +
137D ILE* 4.1 1.0 - - - +
138D THR 3.0 11.3 + - - -
139D TYR 3.2 0.4 + - - -
141D GLN* 1.3 76.0 - - - +
143D LEU* 1.3 58.1 + - - +
145D MET* 3.2 4.5 + - - +
146D ALA 3.0 23.2 + - - -
154D TYR* 3.4 32.3 - - - -
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Residues in contact with LEU 143 (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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139D TYR* 3.0 39.1 + - + +
140D PRO* 3.8 7.9 - - + +
142D GLY* 1.3 73.7 - - - +
144D ALA* 1.3 61.4 + - - +
146D ALA* 3.2 5.1 + - + +
147D LYS* 2.9 29.4 + - + +
154D TYR* 3.6 30.7 - - + +
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Residues in contact with ALA 144 (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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140D PRO 3.2 14.8 + - - +
141D GLN* 3.7 7.4 - - - +
142D GLY 3.3 0.2 - - - -
143D LEU* 1.3 79.2 - - - +
145D MET* 1.3 57.7 + - - +
147D LYS* 3.3 8.8 + - - +
148D GLU* 2.9 29.1 + - - +
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Residues in contact with MET 145 (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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90D PHE* 3.3 65.1 - - + +
93D VAL* 4.1 17.5 - - + -
94D ARG* 3.4 49.1 - - + +
112D LEU* 3.9 14.8 - - + -
141D GLN 3.1 4.6 + - - +
142D GLY 3.4 7.2 - - - +
143D LEU 3.2 0.2 - - - -
144D ALA* 1.3 76.8 - - - +
146D ALA* 1.3 56.5 + - - +
148D GLU* 3.2 16.9 + - - +
149D ILE* 2.9 39.0 + - + +
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Residues in contact with ALA 146 (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* 3.9 8.0 - - + +
142D GLY 3.0 7.7 + - - +
143D LEU* 3.2 11.0 + - + +
145D MET* 1.3 73.4 - - - +
147D LYS* 1.3 66.1 + - - +
149D ILE* 3.1 10.9 + - - +
150D GLY 2.8 20.1 + - - -
151D ALA* 3.0 28.5 + - + +
154D TYR* 3.6 30.3 - - + +
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Residues in contact with LYS 147 (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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143D LEU* 2.9 12.9 + - + +
144D ALA* 3.3 12.5 + - - +
146D ALA* 1.3 77.4 - - - +
148D GLU* 1.3 63.8 + - - +
150D GLY* 3.3 10.5 + - - -
151D ALA 5.5 1.6 - - - -
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Residues in contact with GLU 148 (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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94D ARG* 3.0 53.6 + - - +
98D TYR* 4.9 3.1 + - - -
144D ALA 2.9 13.6 + - - +
145D MET* 3.3 20.7 - - - +
146D ALA 3.1 0.2 - - - -
147D LYS* 1.3 81.0 - - - +
149D ILE* 1.3 64.9 + - + +
150D GLY 3.3 0.9 + - - -
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Residues in contact with ILE 149 (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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80D ILE* 4.9 4.7 - - + -
93D VAL* 4.4 8.7 - - + -
94D ARG* 4.9 3.4 - - - -
98D TYR* 3.2 66.5 + - + -
102D ARG* 4.2 4.2 + - - -
110D ILE* 4.2 13.0 - - + +
112D LEU* 3.9 25.8 - - + -
145D MET* 2.9 33.6 + - - +
146D ALA* 3.3 8.3 - - - +
148D GLU* 1.3 83.4 - - + +
150D GLY* 1.3 62.6 + - - +
151D ALA* 3.7 22.4 - - + -
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Residues in contact with GLY 150 (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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102D ARG* 3.6 19.8 + - - -
110D ILE* 4.8 2.6 + - - +
146D ALA 2.8 5.0 + - - -
147D LYS* 3.3 8.2 + - - -
148D GLU 3.2 4.6 + - - -
149D ILE* 1.3 80.2 - - - +
151D ALA* 1.3 62.8 + - - +
152D VAL* 3.8 3.3 + - - +
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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