Contacts of the strand formed by residues 142 - 151 (chain D) in PDB entry 3KYM
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 ALA 142 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C PHE* 4.0 2.7 - - - -
132D PRO* 5.5 7.6 - - + -
137D THR* 5.2 4.9 - - - +
141D THR* 1.3 72.2 + - - +
143D ALA* 1.3 62.2 + - - +
144D LEU* 5.1 3.3 - - + +
188D VAL 3.9 0.9 - - - +
189D THR* 4.4 0.7 - - - -
190D VAL* 2.4 58.9 + - + +
192D SER* 4.5 7.6 - - - +
195D PHE* 4.3 28.5 - - + -
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Residues in contact with ALA 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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116C PHE* 3.4 29.7 - - + -
118C PHE* 3.2 17.4 - - + -
135C LEU* 3.7 29.4 - - + -
132D PRO* 3.7 13.5 - - - +
142D ALA* 1.3 74.8 - - - +
144D LEU* 1.3 64.3 + - - +
188D VAL 3.6 5.8 - - - -
189D THR* 3.8 15.9 - - + +
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Residues in contact with LEU 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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118C PHE* 3.5 11.0 - - + -
130D LEU 3.1 14.4 - - - +
131D ALA* 6.2 0.2 - - + -
132D PRO* 4.3 11.0 - - + -
142D ALA* 5.1 5.2 - - + +
143D ALA* 1.3 77.5 - - - +
145D GLY* 1.3 58.0 + - - +
160D TRP* 4.2 7.6 - - + -
187D VAL* 3.3 3.8 - - - -
188D VAL* 2.7 46.3 + - + +
190D VAL* 5.5 3.4 - - + -
200D TYR* 3.9 26.5 - - + -
217D VAL* 3.8 28.7 - - + +
219D ARG* 3.3 37.5 - - + +
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Residues in contact with GLY 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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129D PRO 3.7 0.2 - - - -
130D LEU* 2.7 46.9 + - - +
144D LEU* 1.3 76.8 - - - +
146D CYS* 1.3 57.3 + - - -
160D TRP* 3.6 14.1 - - - -
186D SER 3.0 13.5 - - - -
187D VAL* 4.0 1.3 - - - -
217D VAL* 3.5 13.5 - - - +
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Residues in contact with CYS 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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127D VAL* 3.2 25.6 - - + -
128D PHE 3.5 7.0 - - - -
130D LEU* 4.1 2.9 - - - -
145D GLY* 1.3 73.3 - - - -
147D LEU* 1.3 61.3 + - - +
148D VAL* 4.1 6.0 - - + +
158D VAL* 5.9 0.7 - - + -
160D TRP* 3.8 1.5 - - + -
185D SER* 3.0 17.7 + - - -
186D SER* 2.8 27.6 + - - +
202D CYS* 2.0 49.8 - - + -
204D VAL* 5.2 0.2 - - + -
215D LYS* 4.3 11.2 - - - -
217D VAL* 4.8 2.9 - - - -
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Residues in contact with LEU 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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124C GLN* 4.1 11.4 - - - +
131C SER* 3.7 32.3 - - - +
133C VAL* 4.6 16.8 - - + -
178C THR* 5.3 8.5 - - + +
126D SER 3.3 2.3 - - - +
127D VAL* 3.2 8.5 - - - -
128D PHE* 2.7 49.0 + - + +
130D LEU* 4.3 9.4 - - + +
146D CYS* 1.3 73.4 - - - +
148D VAL* 1.3 59.5 + - - +
149D LYS* 3.6 15.1 + - + -
183D SER* 5.2 4.9 - - - +
184D LEU* 3.7 13.7 - - - +
185D SER* 3.4 21.1 - - - +
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Residues in contact with VAL 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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125D PRO* 3.6 30.1 - - + -
126D SER 3.6 3.1 - - - +
127D VAL* 4.7 2.7 - - + -
146D CYS* 4.9 6.3 - - + +
147D LEU* 1.3 74.9 - - - +
149D LYS* 1.3 60.4 + - - +
151D TYR* 4.0 8.3 - - + -
156D VAL* 3.9 18.6 - - + -
158D VAL* 4.3 15.3 - - + -
183D SER* 3.4 6.9 + - - -
184D LEU* 2.8 54.8 + - + +
185D SER* 5.3 0.2 - - - -
186D SER 5.4 1.1 - - - +
204D VAL* 4.0 17.9 - - + -
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Residues in contact with LYS 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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124C GLN* 3.6 21.2 - - - +
129C THR* 4.3 19.2 + - - +
131C SER* 3.7 16.2 - - - +
180C THR* 4.8 10.5 - - - -
125D PRO* 3.1 8.4 - - - +
126D SER* 2.9 33.5 + - - -
128D PHE* 4.1 22.5 - - + -
147D LEU* 3.6 10.0 + - + -
148D VAL* 1.3 75.1 - - - +
150D ASP* 1.3 100.4 + - - +
151D TYR 3.8 0.7 - - - -
177D GLN* 3.3 20.2 - - - +
183D SER* 3.3 12.8 - - - +
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Residues in contact with ASP 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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123D LYS* 3.2 29.6 + - - +
124D GLY 3.2 11.6 - - - +
126D SER* 5.5 2.2 - - - +
128D PHE* 6.1 0.2 - - - -
149D LYS* 1.3 105.8 + - - +
151D TYR* 1.3 58.7 + - - +
177D GLN* 3.1 19.6 - - - +
179D SER* 4.4 3.6 + - - -
181D LEU* 3.8 27.0 - - + +
182D TYR 3.3 11.1 + - - -
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Residues in contact with TYR 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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123D LYS 3.3 8.5 - - - +
125D PRO* 3.6 33.4 - - + -
148D VAL* 4.0 23.3 - - + -
150D ASP* 1.3 75.7 - - - +
152D PHE* 1.3 69.9 + - - +
153D PRO 3.9 11.7 - - - -
154D GLU* 3.8 8.0 + - - -
155D PRO 4.4 3.8 - - - -
156D VAL* 3.6 30.3 - - + +
174D ALA* 3.5 24.4 - - - +
181D LEU* 3.6 4.9 - - - +
182D TYR* 2.8 66.7 + + + +
183D SER* 4.0 4.9 - - - -
184D LEU* 3.9 13.2 - - + +
206D HIS* 3.8 8.7 - + + -
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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