Contacts of the helix formed by residues 175 - 189 (chain D) in PDB entry 2AXT
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 VAL 175 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLN* 4.1 0.2 - - - +
560A CLA 3.4 42.6 - - + +
562A PHO 4.0 16.3 - - + +
73D PHE* 4.1 28.3 - - + +
74D LEU* 3.4 33.6 + - + +
76D VAL 3.9 1.8 + - - -
174D GLY* 1.3 73.7 - - - +
176D ALA* 1.3 63.4 + - - +
178D ILE* 3.2 17.8 + - - +
179D PHE* 3.4 22.4 + - + -
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Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A MET* 4.4 8.3 - - + -
317A TRP* 4.1 16.2 - - + -
318A ALA* 4.5 5.8 - - - +
321A ILE* 3.5 23.5 - - + +
74D LEU 3.2 16.0 + - - +
75D THR* 4.6 3.1 - - - -
175D VAL* 1.3 73.9 - - - +
177D ALA* 1.3 54.9 + - - +
178D ILE 2.5 18.5 + - - -
179D PHE* 2.8 25.3 + - + +
180D ARG* 3.0 12.5 + - - +
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A TRP* 3.8 31.9 - - + +
75D THR 6.2 0.2 - - - -
76D VAL 5.3 0.6 + - - -
77D ALA* 3.7 30.5 - - + -
171D PRO* 4.8 0.3 - - - +
172D SER* 3.9 27.3 + - - -
174D GLY* 3.8 10.7 - - - +
176D ALA* 1.3 76.4 - - - +
178D ILE* 1.3 58.0 - - - +
180D ARG* 4.2 8.4 - - - +
181D PHE* 4.1 10.2 + - - +
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Residues in contact with ILE 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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560A CLA 3.9 57.4 - - + +
562A PHO 4.7 7.4 - - + -
157D PHE* 5.1 3.1 - - + -
171D PRO* 3.9 26.0 - - + -
173D PHE 4.1 14.4 - - - +
174D GLY 3.5 16.3 + - - +
175D VAL* 3.2 13.7 + - - +
176D ALA 2.5 5.7 + - - -
177D ALA* 1.3 78.6 - - - +
179D PHE* 1.3 69.7 + - + +
180D ARG 2.8 4.5 - - - -
181D PHE* 2.5 27.3 + - + +
182D LEU* 2.9 14.9 + - + +
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Residues in contact with PHE 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 3.0 57.7 - - + -
194A MET* 3.7 21.8 - - - -
198A HIS* 6.1 0.7 - - - -
199A GLN* 4.0 4.3 - - - -
321A ILE* 4.1 11.9 - - + -
560A CLA 3.3 49.1 - + + -
175D VAL* 3.5 24.2 - - + -
176D ALA* 2.8 19.9 + - + +
178D ILE* 1.3 86.8 - - + +
180D ARG* 1.3 59.9 + - - +
182D LEU* 3.3 12.6 - - + +
183D LEU* 3.1 30.6 + - - +
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Residues in contact with ARG 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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317A TRP* 3.6 38.1 - - + -
320A ILE* 3.9 8.7 - - + -
321A ILE* 4.5 14.1 - - + +
168D PHE* 5.1 6.7 + - - -
169D PHE* 4.3 22.4 + - - +
170D ALA 5.0 4.4 + - - -
171D PRO* 5.9 0.2 - - - +
176D ALA 3.0 12.8 + - - +
177D ALA 4.2 6.7 - - - +
179D PHE* 1.3 77.2 - - - +
181D PHE* 1.3 88.4 + - - +
182D LEU 3.1 0.2 - - - -
183D LEU* 3.4 5.9 + - - +
184D PHE* 2.9 57.3 + - - +
329D MET* 4.2 5.4 - - + +
333D ASP* 2.6 42.4 + - - +
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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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560A CLA 3.9 10.1 - - + -
156D VAL* 4.2 4.9 - - + -
160D TYR* 4.0 7.9 - + - -
169D PHE 3.5 16.4 - - - -
170D ALA 4.0 0.4 - - - -
171D PRO* 3.3 50.5 - - + -
177D ALA 4.2 4.7 - - - +
178D ILE* 2.5 26.2 + - + +
180D ARG* 1.3 99.2 - - - +
182D LEU* 1.3 56.9 + - - -
184D PHE* 3.9 1.0 - - - +
185D PHE* 3.2 57.8 + + - +
286D VAL* 6.1 0.2 - - + -
354D CLA 3.6 30.1 - - + -
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Residues in contact with LEU 182 (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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193A LEU* 3.6 31.2 - - + -
558A CLA 3.8 26.7 - - + -
560A CLA 3.6 33.7 - - + -
178D ILE* 2.9 14.7 + - + +
179D PHE* 3.3 21.8 - - + +
181D PHE* 1.3 74.8 - - - +
183D LEU* 1.3 66.4 + - - +
185D PHE* 3.0 14.9 + - - +
186D GLN 3.0 9.9 + - - -
354D CLA 3.5 43.4 - - + +
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Residues in contact with LEU 183 (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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187A GLN* 4.3 9.4 - - + -
193A LEU* 3.8 24.0 - - + -
321A ILE* 4.6 8.5 - - + +
324A ALA* 4.2 20.0 - - + -
325A ASN* 4.1 16.4 - - - +
328A MET* 3.5 32.5 - - + -
558A CLA 3.8 19.7 - - + -
179D PHE 3.1 15.4 + - - +
180D ARG* 4.0 4.0 - - - +
182D LEU* 1.3 71.2 - - - +
184D PHE* 1.3 67.5 + - - +
186D GLN* 3.0 8.1 + - + +
187D GLY* 2.7 22.3 + - - -
325D ILE* 4.2 5.9 - - + +
329D MET* 4.6 2.5 - - + -
354D CLA 5.4 0.9 - - + -
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Residues in contact with PHE 184 (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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362B PHE* 3.0 37.9 - + - -
160D TYR* 4.1 5.4 - + - -
169D PHE* 4.8 6.5 - + + -
180D ARG* 2.9 52.2 + - - +
181D PHE* 3.9 4.5 - + - +
183D LEU* 1.3 76.2 - - - +
185D PHE* 1.3 72.4 + + - +
187D GLY* 5.0 0.2 - - - -
188D PHE* 2.8 63.8 + + + +
189D HIS* 3.7 21.5 - - - -
325D ILE* 5.3 0.2 - - - -
329D MET* 4.2 17.2 - - + +
333D ASP* 4.8 2.0 - - - -
334D GLN* 4.3 8.1 - - - -
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Residues in contact with PHE 185 (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 TYR* 3.4 40.4 - + - -
181D PHE* 3.2 51.6 + + - +
182D LEU 3.0 10.6 + - - +
184D PHE* 1.3 86.2 - + - +
186D GLN* 1.3 63.3 + - - +
189D HIS* 2.8 34.8 + + - +
190D ASN 2.8 7.1 + - - -
191D TRP* 4.0 17.5 - + + -
286D VAL* 4.7 13.5 - - + -
289D LEU* 3.2 35.9 - - + -
354D CLA 3.6 20.6 - - + -
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Residues in contact with GLN 186 (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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184A ILE* 3.0 36.3 - - + +
558A CLA 5.9 1.1 - - + -
182D LEU 3.0 7.0 + - - +
183D LEU* 3.0 14.9 + - + +
185D PHE* 1.3 78.1 - - - +
187D GLY* 1.3 56.0 + - - +
190D ASN* 3.2 28.7 + - - +
191D TRP 4.3 0.4 - - - +
192D THR* 2.6 36.7 + - - +
318D ASN* 4.9 1.8 + - - +
322D ASN* 2.6 37.0 + - - +
325D ILE* 4.5 9.0 - - + -
354D CLA 3.3 19.6 - - + +
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Residues in contact with GLY 187 (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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183D LEU 2.7 14.3 + - - -
184D PHE 3.6 2.5 - - - -
186D GLN* 1.3 79.3 - - - +
188D PHE* 1.3 64.0 + - - +
296D TYR* 4.5 0.5 - - - -
322D ASN* 3.5 15.6 - - - +
325D ILE* 3.9 22.2 - - - +
326D ARG* 3.1 27.0 + - - +
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Residues in contact with PHE 188 (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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362B PHE* 3.8 27.9 - + + +
363B PHE* 3.7 31.9 - + - -
364B GLU* 4.7 0.3 - - - +
184D PHE* 2.8 64.2 + + + +
187D GLY* 1.3 78.6 - - - -
189D HIS* 1.3 62.2 + - + +
190D ASN 3.6 0.7 - - - -
294D ARG* 3.2 25.6 + - - +
296D TYR* 3.9 11.3 - - - -
325D ILE* 5.1 0.4 - - + -
326D ARG* 3.6 40.5 + - + +
329D MET* 4.2 12.3 - - - -
330D ALA* 4.6 6.5 - - + -
334D GLN* 3.9 15.5 - - - -
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Residues in contact with HIS 189 (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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362B PHE* 4.9 2.2 - + - -
160D TYR* 2.6 29.2 + + - -
164D GLN* 4.5 2.2 - - - -
184D PHE* 3.7 14.2 - + - -
185D PHE* 2.8 43.9 + + + +
188D PHE* 1.3 73.9 - - + +
190D ASN* 1.3 71.5 + - - +
191D TRP* 3.3 4.0 + - - +
289D LEU* 3.7 38.8 + - + +
292D ASN* 3.2 23.3 - - - -
294D ARG* 3.1 44.0 + - - +
295D SER 4.3 3.5 + - - +
296D TYR* 4.0 3.5 - - - -
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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