Contacts of the strand formed by residues 356 - 367 (chain A) in PDB entry 4H3T
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 LEU 356 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204A GLY* 5.8 1.7 - - - -
205A GLN* 5.7 0.7 - - - +
354A ILE* 3.6 9.0 - - - +
355A ALA* 1.4 86.5 - - + +
357A VAL* 1.3 71.9 + - - +
382A ASP* 4.7 4.9 - - + +
383A THR 3.5 11.7 - - - +
384A PRO* 3.8 24.5 - - + -
385A LEU* 4.2 2.2 - - - -
469A THR* 3.9 44.4 - - + +
472A ALA* 4.3 7.4 - - + -
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Residues in contact with VAL 357 (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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202A PRO* 4.1 10.3 - - + -
203A VAL 3.8 7.2 - - - +
204A GLY* 5.4 1.3 - - - -
213A LEU* 3.9 27.1 - - + -
346A VAL* 4.3 15.7 - - + -
354A ILE* 4.1 7.0 - - + -
356A LEU* 1.3 80.2 - - - +
358A SER* 1.3 60.1 + - - +
359A LEU* 3.8 25.7 + - + -
381A LEU 3.7 0.3 - - - +
382A ASP* 3.7 3.2 - - - -
383A THR* 2.8 36.7 + - - +
385A LEU* 4.1 18.2 - - + -
388A LEU* 4.9 4.7 - - + -
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Residues in contact with SER 358 (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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203A VAL* 2.7 47.2 + - - +
204A GLY 5.7 0.4 - - - -
357A VAL* 1.3 72.3 - - - +
359A LEU* 1.3 60.3 + - - +
360A LEU 3.5 0.5 + - - -
380A ARG* 2.3 52.6 + - - +
381A LEU 3.6 6.0 + - - -
382A ASP* 3.4 19.6 + - - -
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Residues in contact with LEU 359 (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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200A VAL* 4.3 10.3 - - + -
201A ALA 3.5 2.2 - - - +
202A PRO* 3.9 14.8 - - + -
327A LEU* 6.3 0.2 - - + -
330A VAL* 3.8 28.7 - - + -
343A LEU* 3.6 30.3 - - + -
357A VAL* 3.8 21.8 - - + -
358A SER* 1.3 70.8 + - - +
360A LEU* 1.3 61.0 + - - +
361A VAL* 3.7 8.6 + - + +
379A ASP 3.7 0.3 - - - +
380A ARG* 3.2 5.3 - - - -
381A LEU* 2.9 40.0 + - + +
383A THR* 3.6 33.2 - - + +
388A LEU* 5.0 3.6 - - + -
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Residues in contact with LEU 360 (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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50A GLU* 3.7 41.7 - - + +
51A PRO* 4.8 4.3 - - + -
54A LEU* 5.4 5.4 - - + -
199A PHE* 3.8 24.1 - - + +
200A VAL* 3.3 5.7 - - - -
201A ALA* 2.8 34.6 + - + +
203A VAL* 4.2 8.3 - - + -
358A SER 3.5 1.6 + - - -
359A LEU* 1.3 71.6 - - - +
361A VAL* 1.3 59.0 + - - +
362A THR* 4.4 7.6 - - + -
378A TYR* 3.8 28.0 - - + -
379A ASP 3.5 15.9 - - - +
380A ARG* 3.6 21.1 - - + +
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Residues in contact with VAL 361 (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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199A PHE 3.3 8.1 - - - +
200A VAL* 4.1 19.1 - - + -
317A ALA* 3.2 36.3 - - + -
323A VAL* 4.1 24.5 - - + -
330A VAL* 4.8 12.1 - - + -
359A LEU* 4.1 12.3 - - + +
360A LEU* 1.3 78.4 - - - +
362A THR* 1.3 68.5 + - - +
377A ALA* 5.9 0.4 - - + -
378A TYR* 3.3 4.9 + - - -
379A ASP* 2.8 39.3 + - + +
381A LEU* 5.9 1.3 - - + -
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Residues in contact with THR 362 (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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47A PRO* 4.6 6.1 - - + +
48A THR* 6.3 0.7 - - - -
51A PRO* 3.8 28.5 - - + +
167A PHE* 4.6 13.2 - - + -
194A LEU 5.4 1.7 + - - -
197A ILE 4.2 0.6 - - - +
198A GLY* 3.7 1.2 - - - -
199A PHE* 2.9 53.4 + - + +
317A ALA* 5.1 0.3 - - - +
360A LEU* 4.4 7.9 - - + -
361A VAL* 1.3 84.8 - - - +
363A SER* 1.4 63.7 + - - +
376A LEU* 5.6 4.3 - - - -
377A ALA 3.2 11.7 - - - +
378A TYR* 4.3 18.4 - - + -
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Residues in contact with SER 363 (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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167A PHE* 6.2 2.2 - - - -
194A LEU 5.8 0.9 - - - -
197A ILE 4.5 7.0 - - - -
198A GLY* 4.5 5.6 - - - -
316A ARG* 4.4 16.3 - - - +
317A ALA 2.6 37.5 + - - -
319A PRO* 4.3 5.2 - - - +
362A THR* 1.4 76.9 - - - +
364A ALA* 1.3 60.1 + - - +
376A LEU* 3.5 8.0 - - - +
377A ALA* 2.8 40.3 + - - +
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Residues in contact with ALA 364 (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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167A PHE* 5.4 4.9 - - + -
195A ALA* 3.8 24.8 + - + +
197A ILE 5.1 0.6 + - - -
316A ARG* 4.8 12.2 + - - +
319A PRO* 5.5 2.2 - - - -
363A SER* 1.3 79.4 - - - +
365A LYS* 1.3 62.0 + - - +
366A PHE* 3.8 17.5 - - + -
373A LEU* 3.7 21.5 - - + -
375A ASP 3.5 5.8 - - - +
376A LEU* 4.1 7.6 - - + -
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Residues in contact with LYS 365 (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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319A PRO* 4.8 21.2 - - + +
364A ALA* 1.3 73.9 - - - +
366A PHE* 1.3 64.0 + - - +
373A LEU* 3.6 3.8 - - - +
374A ASP* 2.7 37.0 + - + +
375A ASP* 2.9 33.3 + - + +
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Residues in contact with PHE 366 (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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167A PHE* 4.5 8.7 - + - -
168A GLY 4.6 0.7 - - - -
169A SER* 3.9 20.2 - - - -
191A ILE* 4.0 23.3 - - + -
195A ALA* 3.6 35.7 - - + -
364A ALA* 3.8 17.0 - - + -
365A LYS* 1.3 83.5 - - - +
367A GLY* 1.3 58.0 + - - +
370A SER* 3.8 33.6 + - - +
372A THR 3.1 20.6 - - - +
373A LEU* 3.8 26.0 - - + -
374A ASP* 4.2 4.6 - - - +
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Residues in contact with GLY 367 (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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366A PHE* 1.3 73.8 - - - +
368A ASN* 1.3 70.4 + - - -
369A MSE 3.4 2.0 - - - -
370A SER 3.2 3.0 + - - -
371A THR 3.1 5.9 + - - -
372A THR* 2.7 35.2 + - - -
374A ASP* 3.5 18.5 - - - -
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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