Contacts of the helix formed by residues 159 - 170 (chain D) in PDB entry 2J2M
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 ASP 159 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D SER 4.5 0.9 + - - +
150D LYS 5.1 2.0 + - - -
152D ASP* 4.7 7.5 - - + +
155D THR* 5.9 0.2 - - - +
157D ILE 3.5 6.0 + - - +
158D GLN* 1.3 77.4 - - - +
160D PRO* 1.4 68.4 - - - +
161D ASP* 2.9 17.8 + - - +
162D ARG* 3.0 38.7 + - - +
163D TYR* 3.4 12.8 - - - -
449D GLN 4.3 1.0 - - - +
451D ARG* 2.8 41.3 + - - -
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Residues in contact with PRO 160 (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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158D GLN* 4.0 7.6 - - + +
159D ASP* 1.4 88.3 - - - +
161D ASP* 1.3 63.0 + - - +
162D ARG 3.0 1.0 + - - -
163D TYR* 3.4 34.1 - - + +
164D TRP* 3.1 35.0 + - + +
446D ASP* 3.9 25.8 - - - +
449D GLN* 3.9 35.9 - - + +
450D VAL* 4.3 1.1 - - - -
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Residues in contact with ASP 161 (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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387A ARG* 2.7 55.5 + - - -
388A TYR* 4.5 0.9 + - - -
159D ASP* 2.9 16.8 + - - +
160D PRO* 1.3 79.1 - - - +
162D ARG* 1.3 61.7 + - - +
164D TRP* 4.8 0.3 - - - +
165D ASP* 3.5 5.2 + - - +
449D GLN 4.2 2.4 + - - -
450D VAL* 3.6 12.7 - - - +
451D ARG* 2.8 52.6 + - - +
452D HIS* 3.0 23.3 + - - -
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Residues in contact with ARG 162 (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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380A SER* 2.8 23.8 + - - -
382A ASN* 2.5 32.3 + - - -
383A TYR* 3.7 36.8 - - + +
147D HIS 3.0 21.2 + - - -
148D SER* 3.3 20.8 + - - +
150D LYS 3.5 11.5 + - - -
152D ASP* 3.6 33.1 + - - +
153D PRO* 3.4 10.3 - - - +
159D ASP* 3.0 26.2 + - - +
161D ASP* 1.3 81.9 - - - +
163D TYR* 1.3 61.6 + - - +
165D ASP* 3.1 21.5 - - - +
166D PHE 3.2 4.9 + - - -
451D ARG* 5.8 0.2 - - - +
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Residues in contact with TYR 163 (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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148D SER* 3.4 29.2 - - - +
149D LEU* 3.7 28.5 - - + -
158D GLN* 3.7 32.4 + - + -
159D ASP 3.4 16.1 + - - -
160D PRO* 3.4 27.3 - - + +
162D ARG* 1.3 77.6 - - - +
164D TRP* 1.3 71.0 + + - +
166D PHE* 3.2 2.8 + - - +
167D MET* 2.7 46.3 + - + +
177D LEU* 6.4 2.0 - - + -
181D PHE* 4.6 8.6 - + - -
446D ASP* 2.7 37.1 + - - -
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Residues in contact with TRP 164 (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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160D PRO* 3.1 29.1 + - + +
163D TYR* 1.3 87.0 - + - +
165D ASP* 1.3 58.9 + - - +
167D MET* 4.3 8.3 - - + +
168D THR* 2.7 45.8 + - + +
177D LEU* 3.9 27.6 - - + -
181D PHE* 3.7 22.0 - + - -
443D LEU* 4.0 10.5 - - + -
446D ASP* 3.0 25.2 + - + +
447D LEU* 3.6 25.9 - - + +
450D VAL* 3.6 19.3 - - + -
455D THR* 3.7 18.2 - - + -
459D ALA* 4.1 16.6 - - + -
463D PHE* 3.8 30.3 - + - -
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Residues in contact with ASP 165 (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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383A TYR* 2.6 27.1 + - - +
386A ASN* 3.3 2.0 - - - +
387A ARG* 3.0 70.6 + - - +
161D ASP 3.5 4.5 + - - +
162D ARG 3.1 15.3 + - - +
164D TRP* 1.3 77.0 - - - +
166D PHE* 1.3 58.5 + - - +
168D THR* 3.1 15.8 + - - -
169D LEU* 3.2 27.0 - - - +
455D THR* 3.6 7.6 + - - +
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Residues in contact with PHE 166 (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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383A TYR* 4.0 7.3 - + + -
384A GLU 3.6 25.1 - - - -
385A PRO* 4.0 20.1 - - + +
136D ILE* 4.0 20.6 - - + -
141D LYS* 4.0 11.9 - - - -
144D ASP* 3.7 21.5 - - + -
145D MET* 3.7 30.5 - - + -
148D SER* 3.5 27.8 - - - +
162D ARG 3.2 2.8 + - - -
163D TYR 3.6 1.3 - - - +
164D TRP 3.2 0.2 - - - -
165D ASP* 1.3 77.5 - - - +
167D MET* 1.3 89.7 + - + +
169D LEU* 3.1 3.7 + - - +
170D ARG* 3.0 32.8 + - + +
173D SER* 5.9 0.2 - - - -
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Residues in contact with MET 167 (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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135D PHE* 3.6 37.7 - - + -
145D MET* 3.9 10.8 - - + -
148D SER* 4.6 1.3 - - - +
149D LEU* 3.8 37.0 - - + -
163D TYR* 2.7 31.7 + - + +
164D TRP* 4.0 10.8 - - + +
166D PHE* 1.3 89.5 - - + +
168D THR* 1.3 64.0 + - - +
170D ARG 3.1 12.4 - - - +
171D PRO* 3.6 1.6 - - - +
173D SER* 2.9 34.3 + - - +
177D LEU* 4.2 19.5 - - + -
462D ASN* 4.6 0.5 + - - -
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Residues in contact with THR 168 (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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164D TRP* 2.7 38.3 + - + +
165D ASP* 3.1 9.4 + - - -
167D MET* 1.3 73.5 - - - +
169D LEU* 1.3 63.8 + - - +
170D ARG 3.3 0.9 + - - -
171D PRO* 3.8 8.0 - - - +
455D THR* 3.4 32.9 + - + +
458D LEU* 3.8 28.9 - - - +
459D ALA* 3.6 24.9 - - + +
462D ASN* 3.4 20.3 + - - +
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Residues in contact with LEU 169 (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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385A PRO* 3.6 21.3 - - + +
386A ASN 3.3 43.3 - - - +
387A ARG* 4.0 2.5 - - - +
165D ASP* 3.2 24.4 + - - +
166D PHE 3.1 2.7 + - - +
168D THR* 1.3 82.8 + - - +
170D ARG* 1.3 66.6 + - - +
171D PRO* 3.2 9.5 - - - +
458D LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 170 (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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385A PRO* 3.6 31.7 - - - +
20C GLN* 3.7 37.1 + - - +
21C ASN* 5.6 1.0 + - - -
136D ILE* 4.6 3.6 - - + -
137D ARG* 5.8 0.2 - - - +
141D LYS* 4.0 16.3 - - + +
166D PHE* 3.0 35.1 + - + +
167D MET* 3.1 3.8 - - - +
168D THR 3.1 0.2 - - - -
169D LEU* 1.3 81.5 + - - +
171D PRO* 1.4 55.0 - - - +
172D GLU* 2.3 58.0 + - - +
173D SER* 2.9 27.5 + - - -
414D GLU* 4.5 14.5 + - - -
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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