Contacts of the helix formed by residues 192 - 206 (chain A) in PDB entry 3HPD
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 GLY 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A VAL* 3.9 23.0 - - - +
29A THR* 4.7 0.3 - - - +
190A VAL 3.7 0.6 + - - -
191A THR* 1.3 78.8 + - - +
193A THR* 1.3 58.6 + - - +
194A GLY 3.3 2.2 - - - -
195A CYS* 3.2 14.8 + - - +
196A MET* 3.0 30.0 + - - +
300A PO4 5.2 3.1 + - - -
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Residues in contact with THR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A LEU* 3.6 44.9 + - + +
190A VAL* 3.4 34.6 + - + +
192A GLY* 1.3 74.9 - - - +
194A GLY* 1.3 66.9 + - - +
196A MET* 3.1 23.0 + - - +
197A VAL* 3.1 18.3 + - - +
221A PHE* 3.9 15.6 - - + -
242A LEU* 4.6 1.1 - - + -
300A PO4 4.0 11.9 + - - -
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ASP* 3.7 2.0 - - - -
118A LYS* 2.8 37.0 - - - -
165A THR* 5.9 2.2 - - - -
193A THR* 1.3 78.3 + - - +
195A CYS* 1.3 56.8 + - - +
197A VAL* 3.2 8.8 + - - +
198A ALA 3.0 12.1 + - - -
300A PO4 3.0 32.4 + - - -
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Residues in contact with CYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASN* 4.0 9.2 - - - -
26A VAL* 4.0 15.3 - - + -
30A THR* 3.7 4.7 - - + +
61A VAL* 5.6 0.2 - - - +
63A ASN* 3.0 31.4 + - - +
92A ASP* 3.5 8.5 - - - -
94A VAL* 3.8 20.9 - - - -
192A GLY* 3.2 22.0 + - - +
193A THR 3.1 0.2 - - - -
194A GLY* 1.3 77.1 - - - +
196A MET* 1.3 63.3 + - - +
198A ALA* 3.3 3.2 + - - +
199A ALA* 3.0 23.2 + - - +
300A PO4 5.6 1.8 - - - -
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Residues in contact with MET 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A THR* 3.8 22.4 - - + +
30A THR* 4.1 7.4 - - + -
33A ALA* 4.5 17.4 - - + +
190A VAL* 5.0 2.0 - - + -
191A THR 4.9 5.2 - - - +
192A GLY 3.0 17.8 + - - +
193A THR* 3.1 13.4 + - - +
195A CYS* 1.3 77.8 - - - +
197A VAL* 1.3 57.0 + - - +
199A ALA* 3.2 4.0 + - - +
200A LEU* 2.9 35.1 + - - +
221A PHE* 3.8 33.4 - - + -
239A HIS* 3.6 17.9 - - + +
242A LEU* 4.4 10.5 - - + -
243A TYR* 3.2 35.2 - - + +
246A LEU* 5.9 0.4 - - - -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LYS* 3.8 14.4 - - + -
165A THR* 5.9 1.1 - - + -
193A THR 3.1 9.3 + - - +
194A GLY* 3.2 11.9 + - - +
196A MET* 1.3 78.1 - - - +
198A ALA* 1.3 56.8 + - - +
200A LEU* 3.3 8.3 + - - +
201A THR* 2.8 40.4 + - - +
214A THR* 6.0 0.4 - - + -
217A ALA* 4.5 7.2 - - + -
218A LEU* 3.8 36.1 - - + +
221A PHE* 3.4 37.9 - - + -
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Residues in contact with ALA 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A VAL* 3.8 12.0 - - + +
63A ASN* 5.4 1.1 - - - +
90A VAL* 3.6 21.0 - - + +
92A ASP* 3.5 36.6 - - + +
118A LYS* 3.7 10.9 - - + +
194A GLY 3.0 6.1 + - - -
195A CYS* 3.6 6.5 - - - +
196A MET 3.3 0.4 - - - -
197A VAL* 1.3 75.5 - - - +
199A ALA* 1.3 61.7 + - - +
201A THR* 3.3 10.0 + - - -
202A GLY 3.1 15.8 + - - -
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Residues in contact with ALA 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 4.1 3.3 - - - +
20A ASN* 3.9 12.8 - - - +
30A THR* 3.8 25.6 - - + +
33A ALA* 5.7 0.4 - - + -
34A LEU* 3.3 28.1 - - + +
61A VAL* 4.1 13.2 - - + +
195A CYS 3.0 13.4 + - - +
196A MET* 3.2 8.0 + - - +
198A ALA* 1.3 77.9 - - - +
200A LEU* 1.3 62.5 + - + +
202A GLY* 3.1 11.4 + - - -
203A ALA 3.5 2.1 + - - -
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Residues in contact with LEU 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.6 35.0 - - + +
34A LEU* 4.2 9.0 - - + +
37A LEU* 3.7 27.4 - - + -
196A MET 2.9 20.4 + - - +
197A VAL* 3.7 5.4 - - - +
199A ALA* 1.3 74.0 - - - +
201A THR* 1.3 65.9 + - - +
203A ALA* 2.9 15.1 + - - +
204A PHE* 3.1 21.4 + - + -
217A ALA* 4.5 10.5 - - + +
220A THR* 5.7 1.3 - - + -
221A PHE* 3.7 38.8 - - + +
246A LEU* 4.0 17.7 - - + -
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Residues in contact with THR 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.9 17.3 - - + -
116A VAL* 4.0 13.5 - - + -
118A LYS* 5.3 2.1 - - - +
197A VAL* 2.8 29.4 + - - +
198A ALA* 3.4 10.5 - - - -
199A ALA 3.2 0.2 - - - -
200A LEU* 1.3 74.7 - - - +
202A GLY* 1.3 57.4 + - - +
204A PHE* 3.2 2.6 + - - +
205A VAL* 2.8 32.2 + - + +
213A ALA 4.8 0.2 - - - -
214A THR* 3.7 36.8 - - - +
217A ALA* 3.3 19.9 - - - +
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Residues in contact with GLY 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.8 8.6 - - - +
59A ALA* 3.2 23.2 - - - +
61A VAL* 3.8 19.5 - - - -
90A VAL* 3.9 10.1 - - - +
198A ALA 3.1 6.7 + - - -
199A ALA 3.1 11.5 + - - -
201A THR* 1.3 78.1 - - - +
203A ALA* 1.3 60.0 + - - +
205A VAL* 3.3 9.1 - - - +
206A ALA* 3.4 3.5 + - - +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A VAL* 3.8 10.0 - - + +
16A PRO* 3.7 12.7 - - + +
18A VAL* 3.6 9.0 - - - +
34A LEU* 3.8 10.5 - - + -
37A LEU* 4.1 13.7 - - + -
39A ALA* 3.7 29.6 - - + -
199A ALA 3.5 3.4 + - - -
200A LEU 2.9 9.9 + - - +
202A GLY* 1.3 77.0 - - - +
204A PHE* 1.3 63.0 + - - +
206A ALA* 3.3 16.6 + - - +
207A VAL* 3.8 2.3 + - - +
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Residues in contact with PHE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A ILE 4.8 0.7 - - - -
7A ALA* 3.8 11.9 - - + -
8A LEU* 3.7 41.3 - - + -
11A VAL* 3.8 13.2 - - + -
37A LEU* 3.8 23.1 - - + -
200A LEU* 3.1 27.6 + - + -
201A THR 3.2 4.0 + - - +
203A ALA* 1.3 77.9 - - - +
205A VAL* 1.3 55.8 - - - +
207A VAL* 3.0 5.2 + - - +
208A THR* 3.0 30.9 + - + +
213A ALA* 3.4 23.8 - - + +
216A SER* 3.8 21.1 - - - -
217A ALA* 3.7 26.2 - - + -
220A THR* 3.7 22.9 - - - -
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Residues in contact with VAL 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ALA* 4.0 2.5 - - + -
88A PRO* 3.7 37.4 - - + +
89A ILE 5.8 0.2 - - - -
90A VAL* 4.2 11.7 - - + -
115A ASP* 4.8 2.0 - - + -
116A VAL* 4.4 9.0 - - + -
201A THR* 2.8 21.4 + - + +
202A GLY* 3.3 19.5 - - - +
204A PHE* 1.3 72.4 - - - +
206A ALA* 1.3 63.7 + - - +
207A VAL 3.2 0.4 - - - -
208A THR 3.3 20.8 + - - +
210A PRO* 4.0 30.5 - - + -
213A ALA* 3.5 5.8 - - + +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 5.5 0.9 - - - -
16A PRO* 3.7 24.7 - - + -
18A VAL* 5.5 0.2 - - + -
58A ASP* 3.9 30.4 - - + +
59A ALA* 4.2 1.1 - - + -
88A PRO* 4.5 1.8 - - - -
202A GLY 3.4 8.7 + - - +
203A ALA 3.3 12.5 + - - +
204A PHE 3.1 1.2 - - - -
205A VAL* 1.3 80.7 - - - +
207A VAL* 1.3 62.8 + - + +
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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