Contacts of the strand formed by residues 311 - 320 (chain A) in PDB entry 1E8U
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 ARG 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A PHE* 3.4 2.8 - - - -
308A ILE 2.8 38.9 + - - +
309A ASP* 3.6 10.3 - - + +
310A GLY* 1.3 78.6 - - - +
312A VAL* 1.3 59.8 + - - +
313A TRP* 3.2 15.7 - - + +
375A SER* 2.7 38.6 + - - -
376A ILE 2.9 21.3 - - - +
377A LYS* 3.9 24.2 - - - +
378A VAL* 3.7 6.3 - - - -
385A ASP* 3.0 43.4 + - - -
387A VAL* 3.7 11.7 - - - +
434A LYS* 3.4 33.6 - - - +
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Residues in contact with VAL 312 (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 SER* 3.5 30.7 - - - +
243A THR* 4.1 10.1 - - + -
248A ASP* 4.2 10.8 - - + +
272A HIS* 4.3 5.2 - - + +
306A SER 3.5 3.1 - - - +
307A PHE* 4.4 1.1 - - - +
311A ARG* 1.3 73.5 - - - +
313A TRP* 1.3 63.6 + - - +
314A PHE* 3.4 31.9 - - + -
374A LEU 3.7 1.4 - - - +
375A SER* 3.1 4.0 - - - -
376A ILE* 2.7 56.6 + - + +
378A VAL* 3.6 15.8 - - + +
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Residues in contact with TRP 313 (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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305A GLY* 3.1 6.2 - - - -
306A SER 2.8 43.8 + - - +
308A ILE* 3.0 39.7 + - + +
309A ASP* 5.5 2.2 - - + -
311A ARG* 3.2 34.2 + - + +
312A VAL* 1.3 74.8 - - - +
314A PHE* 1.3 60.8 + - - +
373A ILE* 4.0 17.9 - - + -
374A LEU 3.5 3.6 - - - -
375A SER* 3.4 21.5 - - - -
389A THR* 5.3 0.7 - - - -
404A ILE* 3.6 22.1 - - + +
429A MET* 4.3 2.2 - - + -
431A VAL* 3.8 26.5 - - + -
434A LYS* 3.6 28.0 - - - -
435A THR* 3.6 27.4 - - - -
436A ALA* 3.9 9.9 - - + -
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Residues in contact with PHE 314 (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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239A SER* 3.7 39.9 - - - -
240A VAL 3.9 4.7 - - - -
241A SER* 3.9 1.3 - - - -
248A ASP* 3.8 22.0 - - + -
249A MET 4.9 0.7 - - - -
250A LEU* 3.7 43.7 - - + -
272A HIS* 5.0 2.5 - + - -
304A GLY 4.9 0.2 - - - -
305A GLY* 3.7 20.6 - - - -
312A VAL* 3.4 38.1 - - + -
313A TRP* 1.3 76.0 - - - +
315A SER* 1.3 66.1 + - - +
316A VAL* 3.9 2.1 - - + +
373A ILE* 3.5 2.6 - - - +
374A LEU* 2.8 40.7 + - + +
376A ILE* 4.8 10.5 - - + -
404A ILE* 3.9 4.0 - - - -
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Residues in contact with SER 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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239A SER* 4.9 1.1 + - - -
300A PRO* 3.7 1.7 - - - +
301A GLY* 2.9 25.4 + - - -
303A GLY 4.9 2.3 + - - -
304A GLY 5.4 1.6 + - - -
314A PHE* 1.3 77.2 - - - +
316A VAL* 1.3 63.0 + - - +
371A GLN* 4.1 8.5 - - - -
372A ALA 3.7 6.1 - - - -
373A ILE* 4.6 0.7 - - - +
402A GLY* 3.1 31.2 + - - -
403A ARG* 3.5 2.2 + - - -
404A ILE* 3.5 13.7 - - - +
413A LEU* 3.6 30.7 - - - -
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Residues in contact with VAL 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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250A LEU* 4.0 23.3 - - + -
270A MET* 4.5 4.7 - - + -
292A PHE* 4.0 26.7 - - + -
295A TRP* 5.2 1.3 - - + -
298A ASN* 4.5 1.3 - - + -
299A TYR 3.2 21.8 - - - +
300A PRO* 4.2 1.1 - - + -
301A GLY* 4.3 1.3 - - - +
314A PHE 3.9 8.5 - - - +
315A SER* 1.3 80.9 - - - +
317A TYR* 1.3 72.8 + - - +
371A GLN* 3.2 6.7 - - - +
372A ALA* 2.8 44.7 + - + +
374A LEU* 4.1 14.1 - - + -
388A LEU* 4.9 2.2 - - + -
400A ALA 5.0 0.4 - - - -
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Residues in contact with TYR 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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237A SER* 4.5 1.0 + - - -
258A GLU* 4.1 2.6 + - - -
262A TYR* 4.7 5.2 - - - -
295A TRP* 4.0 6.5 - - - -
298A ASN* 3.4 1.7 - - - -
299A TYR* 2.8 48.5 + + + +
300A PRO 3.6 19.3 - - - -
301A GLY* 4.2 1.8 - - - -
316A VAL* 1.3 80.0 - - - +
318A GLY* 1.3 63.0 + - - +
369A ILE* 4.7 5.2 - - + -
370A GLN 3.2 11.9 - - - +
371A GLN* 4.6 0.4 - - - +
399A GLY* 4.0 5.4 - - - -
400A ALA* 3.4 46.0 - - - +
401A GLU* 3.6 21.0 + - + +
1570A SLB 2.9 65.7 + - + +
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Residues in contact with GLY 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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262A TYR* 3.4 21.1 - - - -
295A TRP* 3.5 6.8 - - - -
297A ALA 3.2 14.8 - - - -
299A TYR* 5.2 1.6 - - - -
317A TYR* 1.3 80.6 - - - +
319A GLY* 1.3 58.0 + - - -
369A ILE* 3.2 7.4 - - - +
370A GLN 2.8 27.1 + - - -
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Residues in contact with GLY 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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262A TYR* 3.5 23.0 - - - -
295A TRP* 3.3 10.3 - - - +
296A VAL* 2.8 31.9 + - - -
297A ALA 2.9 9.0 + - - +
318A GLY* 1.3 75.5 - - - -
320A LEU* 1.3 61.4 + - - -
367A LYS* 4.9 2.0 - - - -
368A ARG 3.2 8.3 - - - -
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Residues in contact with LEU 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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294A ASP 3.4 8.7 - - - +
295A TRP* 3.5 44.9 - - + +
296A VAL* 4.3 2.0 - - - -
319A GLY* 1.3 74.0 - - - -
321A LYS* 1.3 66.7 + - - +
322A PRO* 3.4 8.1 - - - +
324A SER* 4.7 0.2 - - - +
326A SER* 4.0 14.8 - - - +
327A ASP* 3.8 38.2 - - + +
330A GLN* 4.5 0.7 - - + -
367A LYS* 3.8 14.2 - - - +
368A ARG* 2.9 26.9 + - + +
370A GLN* 3.7 32.8 - - + +
390A VAL* 5.5 1.3 - - + -
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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