Contacts of the helix formed by residues 178 - 193 (chain D) in PDB entry 1H24
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 TYR 178 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C ALA* 3.8 18.0 - - - -
119C HIS* 3.6 28.3 - + + +
120C SER* 3.9 19.1 - - - -
182C THR* 4.2 11.4 - - + -
276C SER* 4.1 19.3 - - - -
277C ALA* 3.2 18.0 + - - +
278C LYS* 3.2 45.8 + - + -
175D VAL* 2.7 22.7 + - + +
176D PRO 2.7 0.4 - - - -
177D ASP* 1.3 85.2 - - + +
179D HIS* 1.3 64.4 + - - +
180D GLU 2.8 5.2 + - - -
181D ASP* 2.9 11.0 + - + -
182D ILE* 2.9 43.6 + - + +
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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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154C VAL* 4.2 19.9 - - + +
155C PRO* 6.1 3.4 - - + +
175D VAL* 3.3 11.7 + - - -
176D PRO* 3.0 56.8 + - + +
178D TYR* 1.3 74.9 - - - +
180D GLU* 1.3 70.0 + - - +
182D ILE* 4.1 5.9 - - - +
183D HIS* 3.4 21.0 + - - +
317D GLN* 3.6 10.7 + - - +
320D LEU* 3.9 27.6 - - + +
379D LYS* 4.7 5.6 - - - +
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Residues in contact with GLU 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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176D PRO 4.8 1.4 + - - -
178D TYR 2.8 4.8 + - - -
179D HIS* 1.3 79.0 - - - +
181D ASP* 1.3 66.5 + - - +
182D ILE 3.1 1.6 - - - -
183D HIS* 3.3 4.3 + - + +
184D THR* 2.8 31.6 + - - +
379D LYS* 2.7 45.8 + - + +
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Residues in contact with ASP 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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120C SER* 3.6 32.6 + - - +
278C LYS* 4.6 19.1 - - - +
177D ASP 5.5 0.2 - - - +
178D TYR* 2.9 14.8 + - + +
180D GLU* 1.3 78.6 - - - +
182D ILE* 1.3 61.1 + - - +
184D THR* 3.6 6.8 + - - -
185D TYR* 3.2 20.4 + - - +
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Residues in contact with ILE 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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119C HIS 3.5 25.8 - - - +
120C SER 3.8 7.0 - - - +
122C ARG* 3.7 22.2 - - + +
152C PHE* 3.9 27.4 - - + -
154C VAL* 3.8 25.6 - - + -
178D TYR* 2.9 27.5 + - + +
179D HIS* 4.1 5.6 - - - +
181D ASP* 1.3 75.1 - - - +
183D HIS* 1.3 57.3 + - - +
185D TYR* 2.8 24.5 + - - +
186D LEU* 2.8 31.8 + - + +
317D GLN* 4.7 1.8 - - - +
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Residues in contact with HIS 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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179D HIS 3.4 16.4 + - - +
180D GLU* 3.3 7.5 + - + +
182D ILE* 1.3 78.8 - - - +
184D THR* 1.3 68.5 + - - +
186D LEU* 3.2 6.4 + - - +
187D ARG* 3.0 42.9 + - + +
314D PHE* 4.0 21.3 - + - -
317D GLN* 3.4 24.7 + - - +
318D TYR* 4.6 4.4 - + - -
379D LYS* 3.4 42.9 + - + -
380D THR* 4.0 23.7 - - + -
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Residues in contact with THR 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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180D GLU* 2.8 22.2 + - - +
181D ASP* 3.6 8.0 - - - -
183D HIS* 1.3 83.8 - - - +
185D TYR* 1.3 62.4 + - - +
187D ARG* 3.4 8.7 + - + +
188D GLU* 3.1 20.1 + - - +
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Residues in contact with TYR 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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57C GLU* 2.5 48.8 + - - +
120C SER 4.2 6.3 - - - +
121C HIS* 3.3 47.1 - + + +
122C ARG* 3.5 25.1 - - + -
181D ASP 3.2 9.9 + - - +
182D ILE 2.8 10.0 + - - +
184D THR* 1.3 77.5 - - - +
186D LEU* 1.3 72.8 + - + +
188D GLU* 3.0 22.5 + - - +
189D MET* 2.9 45.5 + - + +
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Residues in contact with LEU 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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122C ARG* 3.8 33.9 - - + +
154C VAL* 5.8 2.0 - - + -
182D ILE* 2.8 26.0 + - + +
183D HIS 3.2 4.2 + - - +
185D TYR* 1.3 80.2 - - + +
187D ARG* 1.3 63.4 + - - +
189D MET* 3.1 3.6 + - + -
190D GLU* 3.0 27.5 + - - +
309D PRO* 3.7 12.1 - - + +
313D GLN* 3.4 41.1 - - + +
314D PHE* 3.6 24.9 - - + -
317D GLN* 3.9 22.2 - - + +
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Residues in contact with ARG 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 HIS* 3.0 33.7 + - + +
184D THR* 3.4 11.0 - - + +
186D LEU* 1.3 78.7 - - - +
188D GLU* 1.3 63.6 + - - +
190D GLU* 3.4 32.6 + - - +
191D VAL* 3.9 10.2 + - - +
314D PHE* 4.1 5.8 - - + -
351D LEU* 5.9 0.8 - - - +
353D SER* 3.8 11.6 - - - -
380D THR* 3.2 23.2 + - - +
382D TYR* 2.6 53.1 + - - -
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Residues in contact with GLU 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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184D THR 3.1 9.5 + - - +
185D TYR* 3.0 29.4 + - - +
187D ARG* 1.3 81.1 - - - +
189D MET* 1.3 64.0 + - + +
191D VAL* 3.6 13.4 + - - +
192D LYS* 3.2 43.7 + - - +
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Residues in contact with MET 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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57C GLU* 3.3 24.5 - - - +
122C ARG* 4.7 3.1 - - - +
185D TYR* 2.9 56.6 + - + +
186D LEU* 3.1 1.5 + - - +
188D GLU* 1.3 76.0 - - - +
190D GLU* 1.3 58.6 + - - +
191D VAL 3.0 2.5 - - - -
192D LYS* 2.6 47.1 + - + +
193D CYS* 2.8 34.0 + - - +
305D ASP* 6.3 1.6 - - + -
307D ALA 5.0 5.2 - - - +
309D PRO* 3.6 20.0 - - + -
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Residues in contact with GLU 190 (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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186D LEU 3.0 11.1 + - - +
187D ARG* 3.4 27.0 + - - +
189D MET* 1.3 75.7 - - - +
191D VAL* 1.3 65.2 + - - +
193D CYS* 3.8 1.4 - - - +
194D LYS* 3.2 25.6 + - - +
309D PRO* 3.3 22.5 - - + +
314D PHE* 3.5 9.6 - - - -
351D LEU* 3.8 21.5 - - + +
352D PRO* 3.0 26.6 - - + +
353D SER* 2.4 49.0 + - - -
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Residues in contact with VAL 191 (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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187D ARG 4.0 12.6 - - - +
188D GLU* 3.6 9.1 + - - +
189D MET 3.0 0.8 - - - -
190D GLU* 1.3 81.7 - - - +
192D LYS* 1.3 68.1 + - + +
193D CYS 3.4 0.2 + - - -
194D LYS* 3.5 20.9 + - + +
351D LEU* 4.2 24.9 - - + -
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Residues in contact with LYS 192 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188D GLU* 3.2 42.0 + - - +
189D MET* 2.6 35.4 + - + +
191D VAL* 1.3 82.1 - - + +
193D CYS* 1.3 58.8 + - - +
194D LYS 3.3 4.3 + - - +
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Residues in contact with CYS 193 (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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189D MET* 2.8 33.5 + - - +
190D GLU 3.8 2.9 - - - +
192D LYS* 1.3 78.3 - - - +
194D LYS* 1.3 58.2 + - - +
237D ASN* 3.1 11.6 + - - +
241D ARG* 3.0 55.0 - - - +
305D ASP* 4.9 10.8 - - - -
307D ALA 5.3 1.1 - - - -
308D ALA* 4.1 24.5 - - + -
309D PRO* 4.3 5.6 - - + -
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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