Contacts of the strand formed by residues 170 - 177 (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 VAL 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37C ALA* 4.1 6.7 - - - -
41C ARG* 3.6 23.8 - - - +
160D ILE* 4.6 2.2 - - + +
163D GLU* 3.7 20.0 - - + -
164D ILE* 4.1 14.4 - - + -
168D GLY 3.7 2.9 - - - +
169D PRO* 1.3 72.3 - - - +
171D GLU* 1.3 63.1 + - - +
202D ARG* 3.2 10.2 - - - +
203D ILE* 2.9 51.6 + - + +
246D VAL* 3.3 31.0 - - + -
247D VAL 4.0 4.0 - - - +
248D ALA* 3.7 10.3 - - + -
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Residues in contact with GLU 171 (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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30C TRP 2.8 20.3 - - - +
33C GLY* 3.3 16.7 - - - +
34C ALA* 3.2 15.2 + - - +
37C ALA* 4.4 1.0 - - - +
76D PRO* 3.2 28.4 - - + +
80D TRP* 3.1 25.7 + - + +
170D VAL* 1.3 81.1 - - - +
172D GLY* 1.3 63.7 + - - +
200D ALA* 3.4 15.4 - - - +
201D ILE 3.2 16.2 - - - +
245D GLU 3.5 1.3 - - - +
246D VAL* 3.2 4.9 - - - +
247D VAL* 3.0 40.3 + - + +
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Residues in contact with GLY 172 (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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76D PRO* 6.1 0.9 - - - -
170D VAL 4.0 0.8 + - - -
171D GLU* 1.3 77.4 - - - +
173D ALA* 1.3 62.6 + - - +
200D ALA* 3.2 8.0 - - - +
201D ILE* 2.9 44.2 + - - +
203D ILE* 4.3 6.5 - - - +
245D GLU 3.3 13.5 - - - -
246D VAL* 4.2 9.0 - - - -
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Residues in contact with ALA 173 (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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76D PRO* 5.3 6.7 - - + -
172D GLY* 1.3 77.3 - - - +
174D PHE* 1.3 62.4 + - - +
198D GLY* 5.7 2.5 - - - -
199D HIS 3.4 12.8 - - - +
200D ALA* 4.2 9.4 - - + +
201D ILE* 4.3 1.5 - - - +
241D GLY 2.9 25.6 - - - +
242D ILE* 3.6 7.1 + - - -
245D GLU* 3.4 37.8 + - + +
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Residues in contact with PHE 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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173D ALA* 1.3 75.3 - - - +
175D SER* 1.3 81.1 + - - +
176D VAL* 3.3 21.4 + - + -
180D PHE* 3.8 32.5 - + + -
188D TYR* 5.4 2.7 - + - -
198D GLY* 3.2 6.4 - - - -
199D HIS* 2.9 58.6 + + + +
201D ILE* 3.7 20.6 - - + -
231D PHE* 3.5 31.0 - + - -
233D ILE* 4.2 15.0 - - + -
240D CYS* 3.2 17.5 - - + +
241D GLY* 5.1 0.2 - - - -
242D ILE* 4.1 21.8 - - + +
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Residues in contact with SER 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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174D PHE* 1.3 75.7 - - - +
176D VAL* 1.3 62.5 - - - +
177D TYR* 3.6 31.0 + - - -
188D TYR* 5.5 0.9 + - - -
195D MET* 3.9 19.9 - - - +
197D GLY 3.5 8.2 - - - -
198D GLY* 4.6 0.4 - - - -
240D CYS* 2.7 38.8 + - - +
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Residues in contact with VAL 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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174D PHE* 3.3 20.2 + - + -
175D SER* 1.3 71.8 - - - +
177D TYR* 1.3 69.4 + - - +
180D PHE* 3.9 18.8 - - + -
181D LEU* 4.0 13.7 - - + -
195D MET* 3.6 2.3 - - - +
196D MET* 2.7 46.7 + - + -
197D GLY 2.6 17.1 + - - +
198D GLY 5.1 0.2 - - - -
199D HIS* 3.6 35.2 - - + +
221D TRP* 5.0 4.9 - - + -
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Residues in contact with TYR 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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175D SER* 3.6 37.4 + - - -
176D VAL* 1.3 79.5 - - - +
178D SER* 1.3 68.9 + - - +
179D ASP* 3.0 6.4 + - - +
180D PHE* 3.2 19.1 + - - +
181D LEU* 4.0 3.5 + - - +
188D TYR* 4.2 2.0 + - - +
190D HIS* 3.4 49.9 - + + +
193D GLY 3.5 10.5 - - - +
194D GLU 3.1 5.2 - - - +
195D MET* 3.4 44.4 - - + +
196D MET* 4.5 2.0 - - - -
240D CYS* 3.9 16.5 - - + +
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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