Contacts of the helix formed by residues 173 - 181 (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 SER 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.0 24.5 + - - +
136D ILE* 5.6 0.2 - - - -
167D MET* 2.9 34.6 + - - -
170D ARG* 2.9 18.7 + - - -
171D PRO* 4.0 1.6 - - - +
172D GLU* 1.3 76.7 - - - +
174D THR* 1.3 66.3 + - - +
175D ASN 3.3 0.7 - - - -
176D MET* 3.0 17.5 + - - +
177D LEU* 3.1 28.0 + - - +
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Residues in contact with THR 174 (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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171D PRO* 2.7 23.4 + - - +
172D GLU 3.2 0.4 - - - -
173D SER* 1.3 77.8 + - - +
175D ASN* 1.3 64.1 + - - +
177D LEU* 3.1 15.2 + - - +
178D MET* 3.1 21.0 + - + +
420D ASN 3.8 9.0 - - - -
421D PHE* 3.7 15.6 - - + -
424D ALA* 3.8 16.8 - - + -
462D ASN* 3.8 29.7 + - + +
463D PHE* 4.1 19.5 - - + -
466D ALA* 4.3 3.1 - - + -
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Residues in contact with ASN 175 (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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133D VAL* 3.7 14.9 - - + +
172D GLU 4.2 6.3 + - - +
173D SER 3.3 0.6 - - - -
174D THR* 1.3 79.1 - - - +
176D MET* 1.3 56.4 - - - +
178D MET* 3.2 11.1 - - - +
179D HIS* 2.8 31.4 + - - -
281D THR* 2.9 29.6 + - - +
282D LYS* 5.9 1.8 - - - +
283D ASP* 5.2 0.2 - - - +
420D ASN 4.6 2.8 + - - +
423D GLN* 3.4 20.7 + - + +
424D ALA* 3.2 36.6 - - + +
427D VAL* 3.3 19.7 - - - +
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Residues in contact with MET 176 (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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110D PRO* 4.2 13.9 - - + -
129D ASN* 5.2 1.3 - - + +
131D LEU* 4.0 32.8 - - + -
133D VAL* 3.3 36.0 - - + +
134D PHE* 3.7 15.1 + - + +
135D PHE* 3.5 64.4 - - + +
172D GLU 5.1 0.4 + - - -
173D SER 3.0 10.5 + - - +
175D ASN* 1.3 74.7 - - - +
177D LEU* 1.3 61.5 + - - +
179D HIS* 3.0 5.3 + - - +
180D ILE* 2.9 29.5 + - + +
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Residues in contact with LEU 177 (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* 3.9 24.5 - - + -
163D TYR* 6.4 2.2 - - + -
164D TRP* 3.9 24.0 - - + -
167D MET* 4.2 18.8 - - + -
173D SER* 3.1 46.7 + - - +
174D THR* 3.1 11.0 + - - +
176D MET* 1.3 76.4 - - - +
178D MET* 1.3 61.2 + - - +
180D ILE* 3.9 10.1 - - + -
181D PHE* 3.1 43.4 + - + +
439D LEU* 4.0 0.7 - - - +
463D PHE* 3.6 18.8 - - + -
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Residues in contact with MET 178 (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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174D THR* 3.1 18.4 + - + +
175D ASN* 3.2 10.1 + - - +
177D LEU* 1.3 74.7 - - - +
179D HIS* 1.3 57.7 + - - +
182D THR* 3.2 23.0 - - - +
424D ALA* 3.4 30.5 - - + +
425D GLY* 4.7 0.2 - - - -
427D VAL* 4.0 16.2 - - + -
428D TYR* 3.9 12.6 - - + -
431D MET* 3.4 9.5 - - + +
439D LEU* 3.7 18.8 - - - +
463D PHE* 3.8 17.5 - - + +
466D ALA* 3.6 27.6 - - + -
467D ASP 5.1 0.4 - - - +
470D LEU* 3.7 33.4 - - + -
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Residues in contact with HIS 179 (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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131D LEU* 4.6 13.0 - - + +
132D PRO* 3.9 28.7 - - + +
133D VAL* 3.6 22.7 - - + +
175D ASN* 2.8 32.6 + - - -
176D MET* 3.0 15.5 + - - +
178D MET* 1.3 75.7 - - - +
180D ILE* 1.3 64.7 + - - +
181D PHE 3.2 1.3 - - - -
182D THR* 3.0 27.7 + - - -
184D GLU* 4.5 4.9 - - - +
185D GLY 4.4 3.8 + - - -
194D ARG* 4.5 10.1 - - - -
283D ASP* 4.5 4.7 + - + -
427D VAL* 3.6 34.7 - - + +
431D MET* 5.4 0.7 - - + -
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Residues in contact with ILE 180 (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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108D ARG* 3.2 46.1 + - + +
109D ASP* 4.1 11.7 - - - +
110D PRO* 3.9 17.9 - - + -
131D LEU* 3.9 23.6 - - + -
135D PHE* 4.5 12.1 - - + -
176D MET* 2.9 21.4 + - - +
177D LEU* 3.9 12.3 - - + +
179D HIS* 1.3 75.9 - - - +
181D PHE* 1.3 83.5 + - + +
182D THR 3.4 0.7 - - - -
185D GLY* 3.4 9.4 - - - -
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Residues in contact with PHE 181 (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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108D ARG* 3.5 26.9 - - - +
163D TYR* 4.6 8.1 - + - -
164D TRP* 3.7 17.0 - + - -
177D LEU* 3.1 28.9 + - + +
180D ILE* 1.3 98.9 - - + +
182D THR* 1.3 60.8 + - - +
439D LEU* 3.3 28.9 - - + -
442D ASN* 2.9 42.0 + - + +
443D LEU* 3.8 17.5 - - + -
446D ASP* 2.9 46.9 - - + -
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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