Contacts of the strand formed by residues 314 - 321 (chain A) in PDB entry 1O9S
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 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A PHE* 4.0 17.3 - - - -
195A LYS* 5.3 0.9 - - - -
309A VAL* 4.6 2.7 - - - -
310A HIS* 2.7 45.0 + - - +
312A ARG 3.6 1.6 - - - -
313A PHE* 1.3 73.8 - - - +
315A PRO* 1.3 74.1 - - - +
316A ILE* 3.2 4.2 + - - +
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Residues in contact with PRO 315 (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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193A PHE* 5.7 1.8 - - + -
195A LYS* 5.1 7.9 - - + +
249A ARG* 2.7 42.6 + - - +
269A LEU* 3.7 13.9 - - + +
307A MET* 6.3 3.1 - - + -
308A PHE 3.6 7.9 - - - +
309A VAL* 4.4 14.8 - - + -
314A GLY* 1.3 81.1 - - - +
316A ILE* 1.3 54.3 + - - +
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Residues in contact with ILE 316 (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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244A PHE* 3.9 25.8 - - + -
245A TYR 3.6 17.5 - - - +
246A ASN* 3.8 18.6 - - - +
249A ARG* 3.4 15.3 - - - +
269A LEU* 3.8 15.6 - - - +
275A ILE* 5.2 4.5 - - + -
307A MET* 3.9 4.2 - - - +
308A PHE* 2.9 27.9 + - + +
310A HIS* 3.9 20.0 - - + -
313A PHE* 3.9 12.1 - - + -
314A GLY 3.6 11.7 - - - +
315A PRO* 1.3 81.2 - - - +
317A LYS* 1.3 81.3 + - - +
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Residues in contact with LYS 317 (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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245A TYR* 2.8 29.0 + - + -
267A LEU* 3.8 28.7 - - + -
268A SER 2.7 28.6 + - - +
269A LEU* 3.6 25.5 + - + +
275A ILE* 5.8 1.0 - - - +
305A TYR* 4.2 7.6 - - + -
306A ASP 3.1 17.0 - - - +
307A MET* 3.8 14.4 - - - -
308A PHE* 4.2 2.9 - - - +
316A ILE* 1.3 90.5 - - - +
318A CYS* 1.3 64.4 + - - +
5K GLN* 2.5 39.7 + - - +
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Residues in contact with CYS 318 (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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241A VAL* 4.0 26.2 - - + -
243A SER 3.2 15.5 - - - +
244A PHE* 4.1 7.0 - - + +
245A TYR* 4.3 1.1 - - - +
305A TYR* 3.3 10.4 - - - +
306A ASP* 2.6 50.8 + - - -
307A MET 4.0 9.2 - - - -
308A PHE* 3.8 21.3 - - + -
317A LYS* 1.3 75.1 - - - +
319A ILE* 1.3 67.3 + - - +
320A ARG* 4.5 2.9 - - - -
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Residues in contact with ILE 319 (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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230A LEU* 5.0 3.4 - - + -
241A VAL* 3.6 1.9 - - - -
242A MET* 2.8 33.1 + - + +
243A SER* 2.8 31.7 + - - +
245A TYR* 4.8 1.3 - - + -
292A GLY* 4.0 21.8 - - - +
295A ALA* 4.3 5.2 - - + -
303A CYS* 3.5 32.8 - - + -
304A ILE 3.5 1.8 - - - -
305A TYR* 3.3 38.1 - - + -
318A CYS* 1.3 73.9 - - - +
320A ARG* 1.3 56.8 + - - +
331A LEU* 4.7 13.7 - - + -
333A VAL* 3.6 12.8 - - + -
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Residues in contact with ARG 320 (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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124A PRO 5.0 0.6 + - - -
125A ASP* 3.1 42.2 + - - +
149A PRO* 5.9 0.4 - - - +
239A ASN* 2.8 56.9 + - - +
240A THR 3.3 6.5 - - - +
241A VAL* 3.4 21.2 - - - +
303A CYS* 4.1 2.9 - - - -
304A ILE* 2.9 45.4 + - + +
306A ASP* 3.0 33.9 + - + +
318A CYS* 4.0 5.3 - - - -
319A ILE* 1.3 73.9 - - - +
321A THR* 1.3 68.7 + - - +
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Residues in contact with THR 321 (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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236A VAL* 3.8 19.1 - - + -
237A GLY 2.8 22.2 + - - -
238A PRO* 3.4 0.7 - - - +
239A ASN* 2.9 24.8 + - - -
240A THR 2.9 16.8 + - - +
242A MET* 3.6 26.9 - - + -
302A ASN 3.4 8.1 - - - -
303A CYS* 3.9 7.6 - - - -
319A ILE 4.3 0.2 - - - -
320A ARG* 1.3 79.3 - - - +
322A LEU* 1.3 61.1 + - - +
323A ARG 3.5 11.7 - - - -
325A VAL* 4.0 12.3 - - + -
331A LEU* 5.1 0.9 - - + -
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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