Contacts of the strand formed by residues 195 - 209 (chain D) in PDB entry 1HUC
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 MET 195 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175D SER* 3.9 24.2 - - - +
176D VAL 4.1 5.2 - - - +
177D TYR* 3.4 32.8 - - + +
193D GLY 3.7 0.4 + - - -
194D GLU* 1.3 80.6 + - - +
196D MET* 1.3 64.0 + - - +
197D GLY* 3.8 15.9 - - - +
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Residues in contact with MET 196 (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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111D HIS* 5.4 6.3 - - + +
176D VAL* 2.7 24.1 + - + +
177D TYR 4.4 2.2 - - - +
178D SER* 4.4 12.3 - - - +
181D LEU* 3.5 41.3 - - + -
194D GLU* 3.6 12.3 - - + +
195D MET* 1.3 75.7 - - - +
197D GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 197 (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 PHE 4.1 0.2 - - - -
175D SER* 4.2 4.0 - - - -
176D VAL* 2.6 40.3 + - - +
195D MET* 3.7 14.2 - - - +
196D MET* 1.3 80.7 - - - +
198D GLY* 1.3 57.6 + - - -
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Residues in contact with GLY 198 (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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29C CYS* 4.5 7.8 - - - -
173D ALA* 5.7 2.2 - - - -
174D PHE 3.2 12.8 - - - -
175D SER* 4.6 0.4 - - - -
176D VAL* 5.1 0.4 - - - -
197D GLY* 1.3 71.7 - - - -
199D HIS* 1.3 61.9 + - - -
200D ALA 4.2 0.9 + - - -
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Residues in contact with HIS 199 (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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23C GLN* 3.5 15.9 + - - -
29C CYS* 3.5 22.2 - - + -
173D ALA* 3.4 4.1 - - - -
174D PHE* 2.9 51.8 + + + +
176D VAL* 3.6 17.1 - - + +
180D PHE* 5.0 0.2 - + - -
197D GLY 4.0 0.4 + - - -
198D GLY* 1.3 72.4 + - - -
200D ALA* 1.3 59.4 + - - +
201D ILE* 3.5 17.3 - - + -
219D ASN* 2.5 35.3 + - - -
220D SER* 4.6 0.6 + - - -
221D TRP* 3.4 31.2 + + - -
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Residues in contact with ALA 200 (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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29C CYS* 3.4 38.3 - - - +
30C TRP* 3.8 10.8 - - + +
33C GLY 5.2 0.2 + - - -
76D PRO* 3.9 14.4 - - + -
171D GLU* 3.4 23.6 - - - +
172D GLY 3.2 11.0 - - - +
173D ALA* 4.2 3.8 - - + -
198D GLY 4.2 0.8 + - - -
199D HIS* 1.3 71.0 + - - +
201D ILE* 1.3 71.4 + - - +
220D SER* 4.9 3.3 + - - -
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Residues in contact with ILE 201 (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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33C GLY* 4.2 9.0 - - - -
36C GLU* 5.8 0.4 - - - -
171D GLU* 3.2 11.5 - - - +
172D GLY 2.9 38.6 + - - +
173D ALA 4.3 0.2 - - - +
174D PHE* 3.7 25.8 - - + -
199D HIS* 3.5 23.8 - - + +
200D ALA* 1.3 83.1 - - - +
202D ARG* 1.4 58.3 + - - +
203D ILE* 3.7 20.2 - - + -
217D VAL* 3.6 19.1 - - + -
218D ALA 3.6 15.7 - - - +
219D ASN* 3.9 8.5 - - - +
220D SER 5.4 0.4 - - - +
231D PHE* 4.1 9.0 - - + -
242D ILE* 3.9 16.6 - - + -
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Residues in contact with ARG 202 (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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16C THR 4.0 4.5 + - - -
17C ILE* 3.2 34.4 + - - +
19C GLU 3.2 26.5 + - - -
33C GLY 4.1 4.7 - - - +
36C GLU* 3.8 25.5 + - + +
37C ALA* 3.9 22.2 - - + +
40C ASP* 3.0 28.6 + - - -
169D PRO* 3.6 11.7 - - + -
170D VAL 3.2 13.0 - - - +
201D ILE* 1.4 74.7 - - - +
203D ILE* 1.3 62.3 + - - +
204D LEU* 3.3 18.0 - - - +
217D VAL* 3.3 3.1 - - - -
218D ALA* 2.9 55.7 + - + +
230D PHE* 4.4 3.4 - - - -
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Residues in contact with ILE 203 (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 ILE* 5.1 5.6 - - + -
164D ILE* 4.1 11.9 - - + +
169D PRO* 3.3 4.2 - - - +
170D VAL* 2.9 48.3 + - + +
172D GLY* 4.3 13.5 - - - +
201D ILE* 3.7 23.8 - - + -
202D ARG* 1.3 74.4 - - - +
204D LEU* 1.3 61.4 + - - +
205D GLY 3.7 1.8 - - - +
215D TRP* 3.9 34.8 - - + -
216D LEU 3.5 13.0 - - - +
217D VAL* 4.3 3.8 - - + +
242D ILE* 4.2 28.5 - - + +
246D VAL* 4.4 6.1 - - + -
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Residues in contact with LEU 204 (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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5C PHE* 4.4 0.5 - - - -
6C ASP* 3.8 13.3 - - - +
7C ALA* 3.0 37.8 + - + +
8C ARG* 3.7 29.8 - - + -
17C ILE* 4.2 7.9 - - + +
164D ILE* 4.0 12.6 - - - -
169D PRO* 4.0 11.9 - - + -
202D ARG* 3.3 32.8 - - - +
203D ILE* 1.3 73.2 - - - +
205D GLY* 1.3 59.8 + - - +
216D LEU* 3.1 25.6 + - + +
217D VAL* 3.8 2.7 - - - -
218D ALA* 3.5 26.7 - - + +
230D PHE* 3.9 15.3 - - + -
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Residues in contact with GLY 205 (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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5C PHE* 3.2 12.8 - - - -
164D ILE* 4.1 6.8 - - - +
203D ILE* 3.7 1.6 - - - +
204D LEU* 1.3 84.1 - - - +
206D TRP* 1.3 75.7 + - - +
215D TRP* 3.2 21.0 - - - -
216D LEU* 3.3 22.3 + - - +
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Residues in contact with TRP 206 (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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1C LEU* 3.8 23.3 - - + -
2C PRO* 2.7 35.4 + - + -
3C ALA* 3.4 20.2 - - - -
4C SER* 3.5 3.8 + - - +
5C PHE* 2.9 67.4 + + + +
161D MET* 3.3 62.1 - - + -
164D ILE* 4.6 5.8 - - + -
165D TYR* 4.1 5.8 - + + -
205D GLY* 1.3 83.6 - - - +
207D GLY* 1.3 58.2 + - - +
214D TYR* 3.5 25.6 + - - +
215D TRP* 4.1 4.0 - + + +
216D LEU* 4.1 3.1 - - - +
235D ARG* 3.8 17.5 - - - +
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Residues in contact with GLY 207 (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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3C ALA 3.8 3.8 - - - -
4C SER* 3.7 14.1 - - - -
206D TRP* 1.3 78.3 - - - +
208D VAL* 1.3 63.1 + - - -
214D TYR* 3.0 38.0 + - - -
235D ARG* 2.8 25.7 + - - -
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Residues in contact with VAL 208 (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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3C ALA* 4.2 15.8 + - + +
4C SER* 4.5 2.4 + - - -
207D GLY* 1.3 80.5 - - - +
209D GLU* 1.3 65.0 + - - +
210D ASN 4.6 0.4 - - - +
211D GLY* 3.7 32.8 - - - +
212D THR 3.3 5.8 - - - +
213D PRO* 4.5 5.4 - - + -
214D TYR* 3.3 5.2 + - - -
235D ARG* 3.9 11.9 - - - +
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Residues in contact with GLU 209 (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 GLY* 3.7 16.3 - - - -
187D VAL* 3.4 29.2 - - + +
208D VAL* 1.3 76.0 - - - +
210D ASN* 1.3 66.2 + - + +
212D THR* 2.7 39.0 + - - -
214D TYR* 3.8 5.4 - - + -
232D LYS* 3.2 32.2 + - - +
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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