Contacts of the strand formed by residues 221 - 231 (chain A) in PDB entry 1JZ3
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 GLN 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PHE* 6.0 0.2 - - - -
138A GLN* 3.2 31.3 + - - +
140A ARG* 3.8 10.4 + - - -
217A LYS* 3.6 15.3 - - - +
218A PRO* 2.8 27.5 + - + +
219A THR* 3.9 6.1 + - - +
220A THR* 1.3 75.5 - - - +
222A ILE* 1.3 64.8 + - - +
223A SER* 4.5 7.7 - - - +
246A MET* 3.1 6.2 - - - +
247A CYS* 3.0 53.5 + - + +
315A LEU* 3.5 12.3 - - - -
324A GLU* 3.5 13.9 - - - +
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Residues in contact with ILE 222 (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 PHE* 3.4 5.9 - - + -
217A LYS* 2.8 32.5 + - - +
221A GLN* 1.3 71.2 - - - +
223A SER* 1.3 56.7 + - - +
224A ASP 3.9 18.8 - - - +
225A PHE* 4.2 17.7 - - + -
244A VAL* 4.3 14.6 - - + -
245A GLN 3.6 6.5 - - - +
246A MET* 4.5 0.7 - - - +
256A VAL* 5.9 0.4 - - + -
274A PHE* 6.3 0.2 - - + -
313A VAL* 3.5 35.4 - - + +
315A LEU* 3.8 29.2 - - + +
324A GLU* 2.9 17.2 + - - +
325A ALA 4.5 0.2 - - - -
326A GLU* 3.9 22.9 - - + +
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Residues in contact with SER 223 (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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28A ALA* 6.1 1.4 - - - +
29A ALA 5.0 0.9 - - - +
30A HIS* 3.7 11.4 - - - +
33A PHE* 3.6 15.7 - - - -
221A GLN* 3.3 8.8 + - - -
222A ILE* 1.3 72.3 - - - +
224A ASP* 1.3 63.8 + - - +
245A GLN* 2.9 20.9 + - - +
246A MET 3.5 13.0 + - - -
247A CYS* 3.7 28.6 - - - -
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Residues in contact with ASP 224 (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 ALA 5.2 3.2 - - - +
30A HIS* 4.8 4.7 - - - -
31A PRO* 3.1 22.0 - - - +
33A PHE* 3.9 8.4 - - - -
222A ILE* 3.6 5.4 - - - +
223A SER* 1.3 82.6 + - - +
225A PHE* 1.3 79.1 + - - +
226A HIS* 3.0 30.8 + - - -
245A GLN* 3.0 50.5 + - - +
445A GLN* 4.8 11.7 + - - +
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Residues in contact with PHE 225 (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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31A PRO* 3.4 14.9 - - + +
32A PRO 4.6 4.5 - - - -
33A PHE* 3.8 22.4 - + - -
222A ILE* 4.2 8.7 - - + -
224A ASP* 1.3 81.5 + - - +
226A HIS* 1.3 69.0 + - - +
227A VAL* 4.0 13.2 - - + -
242A ALA* 6.0 0.7 - - + -
243A GLU 3.2 12.3 - - - +
244A VAL* 4.0 17.9 - - + -
245A GLN* 5.5 0.2 - - - -
313A VAL* 4.0 20.2 - - + -
326A GLU* 3.8 21.1 - - + -
327A ALA 3.9 24.5 - - - -
328A CYS* 4.0 21.1 - - + -
449A ASN* 3.0 37.5 + - - -
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Residues in contact with HIS 226 (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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224A ASP* 3.0 28.2 + - - -
225A PHE* 1.3 84.8 - - - +
227A VAL* 1.3 64.8 + - - +
228A ALA* 6.4 0.2 - - + -
241A GLU 3.5 1.7 - - - +
242A ALA* 3.1 5.4 - - - -
243A GLU* 2.9 63.6 + - + +
245A GLN* 3.9 6.3 - - - -
445A GLN* 6.3 1.6 - - - +
448A ARG* 3.4 55.3 + - + +
449A ASN* 3.4 4.9 - - - -
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Residues in contact with VAL 227 (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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225A PHE* 4.0 20.4 - - + -
226A HIS* 1.3 80.4 - - - +
228A ALA* 1.3 63.7 + - - +
240A LEU* 4.0 31.4 - - + -
241A GLU 3.6 2.2 - - - -
242A ALA* 4.5 11.4 - - + -
311A ALA* 5.0 6.1 - - + -
313A VAL* 5.6 1.8 - - + -
328A CYS* 4.1 17.3 - - - -
330A VAL* 4.0 19.7 - - + -
448A ARG 4.8 2.1 - - - +
449A ASN* 2.8 19.7 + - + +
8401A DMS 3.9 23.6 - - + +
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Residues in contact with ALA 228 (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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226A HIS* 5.8 0.4 - - + -
227A VAL* 1.3 75.2 - - - +
229A THR* 1.4 65.8 + - - +
230A ARG* 4.3 9.2 - - + -
239A VAL 4.5 0.4 - - - -
240A LEU* 3.3 6.1 - - - +
241A GLU* 2.9 47.2 + - + +
481A SER* 6.2 3.8 - - - -
8401A DMS 4.6 1.6 - - - -
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Residues in contact with THR 229 (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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227A VAL* 5.1 0.2 - - + -
228A ALA* 1.4 80.6 - - - +
230A ARG* 1.3 61.8 + - - +
231A PHE* 3.5 12.2 - - - -
239A VAL 3.5 4.7 - - - -
240A LEU* 4.4 5.2 - - + -
330A VAL* 4.2 10.5 - - + -
332A PHE* 3.5 45.3 - - + -
333A ARG 3.5 22.7 + - - +
334A GLU* 5.3 1.9 - - - +
8401A DMS 3.3 27.8 - - + +
8409A DMS 5.2 4.9 + - - -
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Residues in contact with ARG 230 (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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228A ALA* 5.3 7.6 - - + -
229A THR* 1.3 79.3 - - - +
231A PHE* 1.4 63.7 + - - +
238A ALA* 3.1 6.1 - - - +
239A VAL* 2.8 59.9 + - + +
241A GLU* 2.8 48.7 + - - +
292A ARG* 4.6 1.6 - - - +
8409A DMS 5.6 6.3 - - + +
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Residues in contact with PHE 231 (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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229A THR* 3.5 24.5 - - - -
230A ARG* 1.4 76.9 - - - +
232A ASN* 1.4 63.2 + - - +
235A PHE* 3.3 41.1 - + + -
237A ARG 3.5 8.1 - - - +
238A ALA* 3.7 23.1 - - + +
298A PRO* 4.1 2.9 - - + -
300A LEU* 3.6 22.7 - - + -
332A PHE* 3.6 15.7 - + + -
333A ARG* 3.5 41.5 - - - -
334A GLU* 3.8 14.2 + - + +
8417A DMS 3.0 23.7 - - - +
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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