Contacts of the strand formed by residues 142 - 153 (chain D) in PDB entry 1Y14
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 ARG 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119C ARG* 5.4 0.8 - - - +
150C ASN* 3.1 32.7 + - - +
151C PHE* 3.5 41.4 - - + -
89D GLY 3.4 3.1 - - - +
90D THR* 3.8 10.0 + - - -
140D LYS 4.5 6.5 - - - +
141D SER* 1.3 77.1 - - - +
143D ILE* 1.3 61.4 + - - +
170D ALA* 3.7 5.0 - - - +
171D ILE* 3.1 48.5 + - + +
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Residues in contact with ILE 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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87D VAL 3.7 1.2 - - - +
88D ASP* 3.3 1.0 - - - -
89D GLY 2.8 35.8 + - - +
91D VAL* 4.3 11.0 - - + -
99D PHE* 3.6 28.7 - - + -
101D VAL* 3.6 35.0 - - + -
137D ILE* 4.0 22.4 - - + -
141D SER* 5.6 1.1 - - - -
142D ARG* 1.3 75.6 - - - +
144D ARG* 1.3 61.6 + - - +
145D VAL* 3.7 6.2 + - + +
163D ILE* 3.7 16.2 - - + -
169D GLY* 3.1 26.0 - - - +
170D ALA* 3.8 1.8 - - - +
171D ILE* 3.7 7.9 - - - +
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Residues in contact with ARG 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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183C LEU* 3.9 10.9 - - - +
184C ALA* 3.0 41.0 + - - +
185C CYS* 4.3 1.6 - - - -
190C GLU* 3.3 20.2 + - - -
194C LEU* 3.8 18.0 - - - +
86D VAL* 3.6 21.5 - - + -
87D VAL 3.4 4.3 - - - +
88D ASP* 2.7 38.5 + - - +
143D ILE* 1.3 71.8 - - - +
145D VAL* 1.3 62.3 - - - +
163D ILE* 3.6 2.9 - - - +
167D TYR 3.4 21.8 - - - +
168D LEU* 3.6 5.8 - - + -
169D GLY 2.8 43.7 + - - +
171D ILE* 3.7 14.4 - - + +
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Residues in contact with VAL 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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85D GLU 3.9 0.5 - - - +
86D VAL* 3.3 4.2 - - - +
87D VAL* 2.8 52.9 + - + +
101D VAL* 4.2 16.8 - - + -
108D VAL* 4.1 25.4 - - + -
110D VAL* 4.2 9.9 - - + -
143D ILE* 3.7 24.2 - - + +
144D ARG* 1.3 79.3 - - - +
146D LYS* 1.3 65.1 + - - +
147D ILE 5.0 0.2 - - - +
162D SER 3.5 10.3 - - - +
163D ILE* 3.6 15.9 - - + -
168D LEU* 4.2 5.4 - - - -
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Residues in contact with LYS 146 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D GLY* 4.0 31.2 - - - +
85D GLU 3.7 2.9 - - - +
86D VAL* 4.4 8.5 - - + +
145D VAL* 1.3 73.7 - - - +
147D ILE* 1.3 68.0 + - - +
148D GLU* 3.1 32.8 + - - +
161D GLY* 3.2 3.1 - - - -
162D SER 2.8 32.2 + - - +
165D GLU* 4.7 19.9 + - + +
168D LEU* 3.7 20.8 - - + +
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Residues in contact with ILE 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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79D PHE* 6.1 0.7 - - + -
81D PRO* 3.8 23.8 - - + -
82D PHE 3.8 9.0 - - - +
83D LYS* 3.6 0.4 - - - -
84D GLY* 2.7 32.7 + - - -
85D GLU* 2.9 37.3 + - + +
87D VAL* 4.4 22.0 - - + -
103D VAL* 6.0 0.4 - - + -
106D MET* 4.7 9.2 - - + -
108D VAL* 4.7 14.8 - - + -
145D VAL* 5.1 0.2 - - + -
146D LYS* 1.3 72.0 - - - +
148D GLU* 1.3 58.8 + - - +
149D GLY 3.7 21.3 - - - +
150D CYS* 3.7 20.2 - - - -
159D ALA* 4.3 5.4 - - + -
160D ILE 3.7 6.5 - - - +
161D GLY* 4.3 1.1 - - - -
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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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151B ILE* 4.0 33.9 - - + +
153B GLN* 3.9 21.0 + - - +
83D LYS* 3.5 31.6 - - - +
114D LEU* 4.4 7.6 - - + -
146D LYS* 3.1 33.1 + - - +
147D ILE* 1.3 73.2 - - - +
149D GLY* 1.3 57.8 + - - +
160D ILE 2.9 11.2 + - - +
161D GLY 4.3 0.9 - - - -
162D SER* 3.5 35.0 + - - +
165D GLU* 5.0 4.7 - - - +
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Residues in contact with GLY 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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151B ILE* 4.9 7.4 - - - -
83D LYS* 4.9 6.7 - - - -
147D ILE* 3.4 4.6 - - - +
148D GLU* 1.3 83.3 - - - +
150D CYS* 1.3 64.5 + - - -
151D ILE* 5.6 1.3 - - - -
159D ALA* 3.4 3.3 - - - -
160D ILE* 2.8 37.9 + - - +
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Residues in contact with CYS 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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81D PRO* 3.8 16.8 - - + +
82D PHE* 3.8 13.2 - - - -
83D LYS* 3.8 20.7 - - - +
147D ILE* 3.7 20.0 - - - -
149D GLY* 1.3 76.7 - - - -
151D ILE* 1.3 65.5 + - - +
152D SER* 3.9 2.8 + - - -
157D ILE* 4.6 10.8 - - + -
158D HIS 3.1 8.5 - - - +
159D ALA* 5.1 0.7 - - - -
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Residues in contact with ILE 151 (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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83B LYS* 6.4 0.9 - - - +
114B LEU* 4.2 11.0 - - + -
148B GLU* 3.9 44.6 - - + +
149B GLY* 4.4 5.6 - - - +
160B ILE* 3.5 43.7 - - + -
149D GLY 4.3 0.6 - - - -
150D CYS* 1.3 76.8 - - - +
152D SER* 1.3 62.4 + - - +
153D GLN* 4.6 9.2 - - - +
157D ILE* 3.6 2.3 - - - +
158D HIS* 2.7 60.3 + - + +
160D ILE* 4.9 9.6 - - + -
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Residues in contact with SER 152 (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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148B GLU* 5.7 0.3 - - - +
40D GLY* 3.6 31.1 + - - -
80D LYS* 6.1 0.9 - - - -
150D CYS* 3.9 3.7 + - - -
151D ILE* 1.3 76.4 - - - +
153D GLN* 1.3 66.9 + - - +
156D SER 3.9 3.4 - - - -
157D ILE* 4.7 5.6 - - - +
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Residues in contact with GLN 153 (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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114B LEU* 4.0 13.7 - - + +
148B GLU* 3.7 24.6 + - - +
162B SER* 5.4 1.0 + - - -
164B LYS* 2.7 41.9 - - - +
165B GLU* 4.0 13.0 + - - +
40D GLY* 3.1 21.0 + - - -
151D ILE* 4.6 2.5 - - + +
152D SER* 1.3 77.0 - - - +
154D VAL* 1.3 67.5 + - - +
155D SER 3.3 0.9 - - - +
156D SER* 2.9 25.3 + - - +
158D HIS* 3.3 26.7 - - + +
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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