Contacts of the strand formed by residues 338 - 348 (chain A) in PDB entry 5E97
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 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A ASP 4.4 6.8 + - - +
292A SER* 3.4 15.1 - - - +
293A VAL* 2.8 33.1 + - - +
336A GLY 3.4 10.3 + - - +
337A LYS* 1.3 78.9 - - - +
339A VAL* 1.3 54.8 + - - +
340A TRP* 4.2 1.3 - - + +
376A GLY 6.0 1.8 - - - +
378A GLU* 3.5 44.5 + - + +
51B LEU 5.4 4.8 + - - -
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Residues in contact with VAL 339 (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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293A VAL* 3.5 8.3 - - + +
295A TRP* 3.5 20.6 - - + +
326A VAL* 3.8 11.0 - - + -
327A PHE* 3.5 33.4 - - + -
330A VAL* 3.9 24.7 - - + -
337A LYS 3.6 9.4 + - - +
338A LYS* 1.3 79.5 - - - +
340A TRP* 1.3 65.1 + - - +
376A GLY 5.0 3.2 + - - -
377A ILE* 3.4 25.3 - - + -
378A GLU* 3.0 26.4 + - - +
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Residues in contact with TRP 340 (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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185A ILE* 4.2 0.9 - - + -
264A TYR* 3.4 46.2 - + - -
292A SER* 3.2 28.4 + - - -
293A VAL 2.8 12.9 + - - +
294A THR* 3.3 14.2 - - + -
295A TRP* 3.2 31.3 + - - -
338A LYS* 4.2 0.6 - - - +
339A VAL* 1.3 84.6 - - - +
341A LEU* 1.3 60.6 + - - +
377A ILE* 4.4 0.7 - - - -
378A GLU* 2.9 28.1 + - + +
379A VAL* 3.4 38.4 - - + +
381A MET* 3.4 29.6 - - + -
53B SER* 5.8 0.7 - - - -
91B TYR* 3.5 25.6 - + - -
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Residues in contact with LEU 341 (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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295A TRP* 3.4 39.0 - - + +
296A HIS* 4.1 0.4 - - - -
297A HIS* 3.8 28.3 - - + +
319A PHE* 3.6 29.4 - - + -
340A TRP* 1.3 71.8 - - - +
342A GLY* 1.3 59.3 + - - +
343A GLU 3.4 1.6 - - - -
344A THR* 3.9 23.8 - - + +
368A LYS* 4.0 5.2 - - + -
372A SER* 3.8 11.7 - - - +
377A ILE* 3.8 6.6 - - + +
379A VAL 2.9 13.3 + - - +
380A VAL* 3.6 13.0 - - + -
381A MET* 2.8 33.1 + - - +
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Residues in contact with GLY 342 (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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221A GLU* 5.3 0.4 - - - -
267A ASP* 4.1 12.8 - - - -
294A THR* 4.2 11.4 - - - -
295A TRP 2.8 13.9 + - - -
296A HIS* 3.9 3.8 - - - -
340A TRP 3.4 4.6 + - - -
341A LEU* 1.3 71.1 - - - +
343A GLU* 1.3 60.6 + - - +
381A MET* 3.5 29.6 - - - +
60B THR* 4.2 0.3 - - - +
93B ARG* 3.6 17.7 + - - -
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Residues in contact with GLU 343 (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 ASN* 3.3 2.4 - - - +
296A HIS* 3.2 31.6 - - + +
297A HIS 3.2 20.6 + - - -
298A TYR* 2.5 31.5 + - - +
341A LEU 3.4 1.8 + - - -
342A GLY* 1.3 80.5 - - - +
344A THR* 1.4 63.1 + - - +
381A MET 3.4 6.7 - - - -
383A GLN* 3.7 20.9 - - + +
60B THR* 4.5 2.9 - - + -
93B ARG* 2.7 26.9 + - - +
96B GLY* 3.8 3.5 - - - -
1C BDP 2.7 36.5 + - - +
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Residues in contact with THR 344 (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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297A HIS* 2.7 22.9 + - - +
298A TYR* 4.6 1.8 - - - -
341A LEU* 3.9 14.0 - - + +
343A GLU* 1.4 80.1 - - - +
345A SER* 1.3 59.3 + - - +
365A TRP* 4.2 5.2 - - + -
368A LYS* 2.7 32.3 + - + +
380A VAL* 3.6 27.8 - - + -
381A MET 3.0 17.4 + - - +
382A ARG* 3.6 5.4 - - - -
383A GLN* 2.8 25.7 + - - +
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Residues in contact with SER 345 (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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297A HIS 3.2 3.8 + - - -
298A TYR* 3.4 34.1 - - - -
299A TYR* 3.8 1.7 + - - -
344A THR* 1.3 79.3 + - - +
346A SER* 1.3 70.2 + - - +
347A ALA 3.5 0.2 - - - -
365A TRP* 5.9 2.5 - - - -
368A LYS* 3.2 20.5 + - - +
382A ARG* 3.5 12.4 + - - +
383A GLN* 2.7 23.0 + - - -
391A TYR* 3.3 22.0 - - - +
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Residues in contact with SER 346 (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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299A TYR* 3.0 34.5 + - - +
300A LEU* 3.4 3.3 + - - +
310A PHE* 3.8 12.6 - - - -
345A SER* 1.3 81.0 + - - +
347A ALA* 1.3 60.9 + - - +
356A SER* 2.8 33.8 + - - -
361A ALA* 5.4 4.7 - - - -
364A MET* 3.7 31.8 - - - +
382A ARG* 5.7 2.1 + - - -
391A TYR* 4.3 1.9 - - - +
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Residues in contact with ALA 347 (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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298A TYR* 3.6 6.2 - - - -
300A LEU* 3.0 22.0 - - + +
301A ASN 4.1 0.9 - - - +
302A GLY* 3.6 22.9 - - - +
305A ALA* 4.8 0.4 - - + -
310A PHE* 4.8 3.4 - - + -
345A SER 3.5 0.4 - - - -
346A SER* 1.3 85.1 + - - +
348A TYR* 1.3 59.8 + - - +
351A GLY* 3.3 4.7 + - - -
352A ALA* 4.0 16.4 - - + +
356A SER* 4.3 1.1 - - - +
391A TYR* 3.1 27.2 - - - -
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Residues in contact with TYR 348 (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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298A TYR* 3.6 12.0 - - + -
300A LEU* 3.0 33.2 + - - -
301A ASN* 3.5 38.5 + - - +
302A GLY* 2.8 26.7 + - - -
303A ARG* 5.6 4.5 - - - -
347A ALA* 1.3 71.8 - - - +
349A GLY* 1.3 67.1 + - - +
350A GLY 3.2 1.6 - - - -
351A GLY 3.4 1.7 + - - -
612A NPO 3.5 56.6 + + + -
1C BDP 3.4 18.8 - - - +
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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