Contacts of the strand formed by residues 334 - 342 (chain A) in PDB entry 3S3J
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 PHE 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A TYR 4.3 1.1 - - - -
169A GLN* 3.8 24.0 - - + -
170A GLY 3.2 32.8 - - - -
277A CYS* 3.9 9.6 - - - -
278A TRP* 3.9 32.8 - + - -
299A THR* 4.1 6.3 - - + -
300A ASN 3.2 13.2 - - - +
301A TYR* 3.7 17.7 - - + -
302A ASN* 4.7 1.3 - - - +
332A TRP* 3.2 20.7 - - - +
333A ASN* 1.3 86.3 - - - +
335A HIS* 1.3 60.8 + - - +
336A CYS* 3.9 19.3 - - - -
277B PHQ 3.7 28.5 - + - -
278B 02Y 3.3 15.6 - - + +
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Residues in contact with HIS 335 (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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277A CYS* 3.6 10.6 - - + +
299A THR* 3.4 1.2 - - - -
300A ASN* 2.8 44.5 + - - +
302A ASN* 5.3 2.9 - - - +
332A TRP* 4.4 15.4 - + + -
334A PHE* 1.3 75.6 - - - +
336A CYS* 1.3 83.2 + - - +
337A TRP* 3.6 23.4 - + + -
358A ASP* 2.8 23.4 + - - -
360A THR* 3.6 30.9 - - + +
396A GLU* 3.3 34.8 + - - +
278B 02Y 4.1 4.2 - - - +
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Residues in contact with CYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ILE* 4.5 3.1 - - - -
168A TYR 3.9 8.5 - - - -
277A CYS* 3.6 10.6 - - - +
278A TRP* 3.7 40.2 - - - -
281A ALA* 4.1 9.7 - - + +
297A VAL* 4.7 3.1 - - + -
298A VAL 3.1 8.7 - - - +
299A THR* 3.4 22.0 - - - -
334A PHE* 3.9 8.1 - - - -
335A HIS* 1.3 100.0 + - - +
337A TRP* 1.3 64.9 + - - +
358A ASP* 4.2 0.3 - - - +
359A PRO* 5.3 0.3 - - - +
360A THR* 4.1 6.9 + - - -
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Residues in contact with TRP 337 (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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281A ALA* 3.8 10.3 - - - +
297A VAL* 3.6 5.0 - - - -
298A VAL* 2.9 44.0 + - + +
300A ASN* 3.6 31.4 - - + -
335A HIS* 3.6 34.8 - + + -
336A CYS* 1.3 75.5 - - - +
338A VAL* 1.3 89.9 + - - +
356A ALA* 3.7 13.4 - - + +
357A LEU 3.3 11.9 - - - +
358A ASP* 4.0 20.2 - - + -
359A PRO* 4.6 3.1 - - - -
393A VAL* 4.7 9.9 - - + -
396A GLU* 4.1 13.7 - - + -
397A VAL* 3.8 17.3 - - + -
426A ILE* 5.1 2.2 - - + -
443A TYR* 3.0 43.1 + + - -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ALA* 3.3 31.9 - - + +
284A ALA* 4.2 11.9 - - + -
285A CYS* 4.2 8.3 - - + +
288A LEU* 4.1 13.0 - - + -
295A THR* 3.8 16.8 - - + -
296A ARG 3.4 10.8 - - - +
297A VAL* 4.5 1.8 - - + -
298A VAL 4.6 0.2 - - - +
337A TRP* 1.3 86.3 - - - +
339A GLU* 1.3 63.9 + - - +
340A SER* 4.3 0.2 - - - +
356A ALA* 3.3 5.0 - - - -
357A LEU* 2.8 61.6 + - + +
359A PRO* 5.1 1.6 - - + -
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Residues in contact with GLU 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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295A THR* 3.2 6.1 - - - +
296A ARG* 2.8 70.0 + - + +
298A VAL* 3.7 17.0 - - + +
338A VAL* 1.3 78.7 - - - +
340A SER* 1.3 61.8 + - - +
354A TRP* 3.7 20.0 - - + -
355A GLN 3.0 6.5 - - - +
356A ALA* 4.5 0.9 - - - -
376A VAL* 3.4 16.5 - - + +
439A ILE* 3.8 4.0 - - - +
442A THR* 4.7 0.5 + - - -
443A TYR* 2.6 44.0 + - - +
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Residues in contact with SER 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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288A LEU* 3.5 13.0 - - - +
293A ILE* 3.8 9.4 - - - +
294A PRO 3.2 5.4 - - - -
295A THR* 2.8 29.1 + - - +
339A GLU* 1.3 72.1 - - - +
341A TRP* 1.3 59.2 + - - +
342A MET* 3.6 19.1 - - - -
354A TRP* 3.6 4.7 - - - -
355A GLN* 2.7 45.9 + - - +
357A LEU* 4.0 13.3 - - - +
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Residues in contact with TRP 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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147A ALA 5.5 0.2 + - - -
148A VAL* 3.6 28.9 - - - +
149A TYR 2.8 29.2 + - - -
150A LEU* 3.5 28.0 - - + +
151A ASP* 6.1 0.9 - - - -
155A GLU* 5.9 1.1 - - - -
293A ILE* 4.4 1.1 - - - +
294A PRO* 2.9 29.0 + - + +
340A SER* 1.3 71.3 - - - +
342A MET* 1.3 70.9 + - - +
352A GLU* 6.3 1.8 - - + -
353A GLY* 3.4 39.9 - - - -
354A TRP* 3.5 41.7 - + + -
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Residues in contact with MET 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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147A ALA 3.2 13.5 - - - +
148A VAL* 4.3 0.7 - - + +
217A PRO* 3.7 23.6 - - + +
218A VAL* 3.5 41.5 - - + -
221A GLY* 5.8 0.4 - - - -
293A ILE* 4.2 8.7 - - + -
340A SER* 3.6 39.7 - - - +
341A TRP* 1.3 83.6 - - - +
343A THR* 1.3 72.8 + - - +
344A ARG* 4.2 0.7 - - - -
352A GLU* 4.6 0.7 - - - -
353A GLY 2.9 29.1 + - - +
355A GLN* 3.4 22.4 + - + -
357A LEU* 5.4 2.7 - - + -
373A PRO* 4.8 6.5 - - + -
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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