Contacts of the strand formed by residues 16 - 24 (chain D) in PDB entry 1ZQ1
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 LYS 16 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14D GLY* 3.7 11.9 - - - +
15D LEU* 1.3 80.7 - - - +
17D VAL* 1.3 61.5 + - - +
194D PRO* 3.1 32.2 + - + +
195D ASP* 4.6 13.1 + - - +
196D ILE 3.6 0.7 - - - -
231D ASN 3.6 5.2 - - - +
232D VAL* 3.6 1.4 - - - -
233D SER* 3.1 43.6 + - - +
239D ARG* 5.1 3.5 + - - +
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Residues in contact with VAL 17 (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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15D LEU* 3.6 27.6 - - + -
16D LYS* 1.3 79.7 - - - +
18D GLY* 1.3 71.5 + - - +
193D THR 2.9 16.6 - - - +
194D PRO* 3.2 6.4 + - - +
196D ILE* 2.7 47.5 + - + +
198D HIS 5.0 1.6 - - - +
202D ALA* 4.4 2.2 - - + -
230D LEU* 3.9 9.0 - - + -
231D ASN 3.6 5.6 - - - +
232D VAL* 4.1 4.5 - - + -
255D ILE* 3.6 40.2 - - + -
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Residues in contact with GLY 18 (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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17D VAL* 1.3 82.5 - - - +
19D LEU* 1.3 63.2 + - - +
20D GLU* 5.6 0.4 - - - -
192D THR* 4.7 0.7 - - - -
193D THR 3.8 12.1 - - - -
194D PRO* 3.8 10.0 - - - +
196D ILE* 5.1 0.4 - - - -
230D LEU* 3.6 5.9 - - - +
231D ASN* 2.8 43.4 + - - +
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Residues in contact with LEU 19 (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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18D GLY* 1.3 73.5 - - - -
20D GLU* 1.3 64.5 + - - +
21D ILE* 4.5 17.0 - - + -
190D ILE 3.9 0.6 - - - +
191D SER* 3.3 1.4 - - - -
192D THR* 2.5 58.6 + - + +
196D ILE* 4.6 7.0 - - + -
202D ALA 4.1 7.0 - - - +
205D VAL* 4.3 7.4 - - + -
206D ALA* 3.7 42.4 - - + +
209D ILE* 5.0 0.7 - - + -
228D GLN* 5.2 4.0 - - + +
229D ASP 3.2 22.2 - - - +
230D LEU* 3.2 25.4 - - + -
251D ILE* 4.9 5.2 - - + -
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Residues in contact with GLU 20 (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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18D GLY 5.6 0.2 - - - -
19D LEU* 1.3 83.4 - - - +
21D ILE* 1.3 63.1 + - - +
22D HIS* 4.4 11.1 - - + +
189D GLU* 5.3 7.1 - - + +
190D ILE 3.2 5.6 - - - +
191D SER* 3.9 20.6 - - - -
227D ARG 3.8 0.9 - - - +
228D GLN* 3.4 2.1 - - - -
229D ASP* 2.8 54.2 + - + +
231D ASN* 5.6 7.4 - - - +
241D GLU* 5.7 6.6 - - - +
243D LYS* 5.0 7.1 + - - -
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Residues in contact with ILE 21 (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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19D LEU* 4.5 10.5 - - + -
20D GLU* 1.3 82.3 - - - +
22D HIS* 1.3 71.7 + - - +
23D ARG* 5.1 0.2 - - + -
188D ILE 3.2 2.1 - - - +
189D GLU* 3.2 4.1 - - - +
190D ILE* 2.7 48.2 + - + +
206D ALA* 4.3 11.9 - - - +
209D ILE* 3.9 37.2 - - + -
210D GLY* 5.3 1.1 - - - +
213D LEU* 4.6 18.6 - - + -
226D ILE* 4.8 6.3 - - + -
227D ARG 3.1 9.4 - - - +
228D GLN* 3.8 33.4 - - + +
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Residues in contact with HIS 22 (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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20D GLU* 5.2 7.2 - - + +
21D ILE* 1.3 79.4 - - - +
23D ARG* 1.3 63.1 + - - +
162D GLU* 3.4 16.0 + - - -
187D LEU* 4.5 15.3 - - + +
188D ILE 3.1 5.7 + - - -
189D GLU* 2.9 49.9 + - + +
225D THR 3.9 0.6 - - - +
226D ILE* 3.7 1.6 - - - -
227D ARG* 2.6 64.7 + - + +
229D ASP* 4.8 11.4 + - - -
243D LYS* 6.1 0.8 + - - -
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Residues in contact with ARG 23 (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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21D ILE* 5.1 0.9 - - + -
22D HIS* 1.3 74.0 - - - +
24D GLN* 1.3 64.3 + - - +
25D LEU 3.6 0.3 + - - -
187D LEU* 3.5 5.3 - - - +
188D ILE* 2.8 54.5 + - + +
210D GLY* 4.8 6.7 + - - -
213D LEU* 3.9 33.7 - - + +
214D ARG* 5.3 3.2 - - - +
219D VAL* 3.3 30.5 - - + +
220D LYS 2.9 28.3 + - - -
221D ARG* 4.1 11.7 - - - +
225D THR 3.4 9.8 + - - -
226D ILE* 3.0 53.3 - - + +
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Residues in contact with GLN 24 (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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23D ARG* 1.3 76.6 - - - +
25D LEU* 1.3 60.6 + - - +
38D LEU* 5.9 2.9 - - - +
164D ASP* 3.0 25.3 + - - +
182D ARG* 4.1 10.9 - - - +
185D ILE* 3.5 34.6 - - + +
186D PRO 3.3 9.2 - - - +
187D LEU* 3.7 11.9 - - + -
219D VAL* 3.6 7.6 - - - +
220D LYS* 3.1 39.6 + - + +
224D GLY 4.9 2.0 - - - +
225D THR* 3.5 33.6 + - + +
227D ARG* 3.8 8.6 - - - +
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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