Contacts of the strand formed by residues 338 - 349 (chain A) in PDB entry 1V9P
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 VAL 338 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A PHE* 4.0 20.4 - - + -
331A GLN 3.1 15.9 - - - +
332A VAL* 4.2 9.4 - - + +
336A GLY 3.6 11.7 - - - +
337A ARG* 1.3 73.1 + - - +
339A THR* 1.3 57.2 + - - +
340A PRO* 4.2 0.3 - - - +
362A GLU* 4.9 1.7 - - - +
405A TRP* 2.9 43.0 + - + +
406A PRO* 4.9 5.2 - - + -
409A CYS* 5.4 0.4 - - - -
410A PRO* 5.0 11.0 - - + -
416A LEU* 3.6 30.7 - - + -
423A HIS 2.9 14.1 + - - +
424A ARG* 4.0 4.7 - - - -
425A CYS* 4.4 2.2 - - + +
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Residues in contact with THR 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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190A GLU* 5.4 1.1 - - - +
330A PHE* 3.3 9.0 - - - -
331A GLN* 2.6 44.2 + - + +
332A VAL 5.8 0.2 - - - -
333A GLY* 4.8 5.3 + - - -
337A ARG* 3.1 33.4 + - - +
338A VAL* 1.3 71.2 - - - +
340A PRO* 1.3 86.6 - - + +
341A VAL* 4.7 7.6 - - + -
358A THR* 4.6 8.1 - - - +
360A HIS 3.8 4.9 - - - +
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Residues in contact with PRO 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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328A VAL* 4.8 0.9 - - + -
330A PHE* 3.8 23.1 - - + -
337A ARG* 4.4 0.4 - - - +
338A VAL 4.2 3.6 - - - +
339A THR* 1.3 90.6 - - + +
341A VAL* 1.3 65.9 + - - +
358A THR* 3.8 1.0 + - - -
359A LEU* 2.9 33.0 + - + -
360A HIS 2.5 47.6 - - - +
361A ASN* 3.8 11.4 - - - +
365A ILE* 3.9 9.0 - - + -
405A TRP* 3.9 9.4 - - + -
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Residues in contact with VAL 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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328A VAL* 3.3 6.1 - - - +
329A VAL* 2.8 58.8 + - + +
331A GLN* 3.7 34.5 - - + +
339A THR* 4.7 6.7 - - + -
340A PRO* 1.3 80.7 - - - +
342A GLY* 1.3 71.2 + - - +
343A VAL* 3.6 0.6 + - + -
356A ARG* 4.5 17.9 - - + -
357A VAL 3.6 15.3 - - - +
358A THR* 4.8 5.8 - - - +
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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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325A LEU* 4.7 5.6 - - - -
327A ASP 4.0 4.7 - - - -
328A VAL* 4.3 1.1 - - - -
341A VAL* 1.3 73.6 - - - +
343A VAL* 1.3 61.9 + - - -
344A LEU* 3.6 5.6 + - - -
356A ARG* 3.4 2.3 - - - -
357A VAL* 2.5 50.0 + - - +
359A LEU* 3.5 23.5 - - - +
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Residues in contact with VAL 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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325A LEU* 4.9 0.2 - - - -
326A LEU* 3.0 29.3 + - + +
327A ASP* 2.8 30.3 + - + +
329A VAL* 4.0 25.1 - - + -
341A VAL 4.4 3.6 - - - +
342A GLY* 1.3 72.8 - - - -
344A LEU* 1.3 65.5 + - - +
355A SER* 3.6 10.5 - - - +
356A ARG* 3.7 32.1 - - + +
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Residues in contact with LEU 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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323A THR* 4.3 13.5 - - + -
324A ARG 3.4 7.6 - - - +
325A LEU* 4.1 25.8 - - + -
326A LEU* 4.3 5.1 - - - +
342A GLY 4.1 2.9 - - - +
343A VAL* 1.3 84.3 - - - +
345A GLU* 1.3 69.8 + - - +
346A PRO* 3.5 6.4 - - - +
347A VAL* 5.8 0.4 - - + -
354A VAL* 4.2 19.3 - - + +
355A SER* 2.8 23.5 + - - +
357A VAL* 3.5 42.6 - - + -
359A LEU* 6.1 0.2 - - + -
376A VAL* 4.3 12.1 - - + -
378A VAL* 4.3 16.8 - - + -
388A VAL* 5.7 2.5 - - + +
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Residues in contact with GLU 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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323A THR* 3.0 26.7 + - - +
324A ARG* 3.0 22.2 + - + +
326A LEU* 3.7 29.0 - - + +
344A LEU* 1.3 74.9 - - - +
346A PRO* 1.3 95.2 - - + +
347A VAL* 2.9 5.7 + - - +
354A VAL 3.8 2.6 - - - +
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Residues in contact with PRO 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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326A LEU* 5.2 2.2 - - + -
344A LEU 3.5 6.0 - - - +
345A GLU* 1.3 104.6 - - + +
347A VAL* 1.3 59.4 + - - +
348A PHE* 5.0 4.5 - - + -
353A GLU* 3.5 25.4 - - + +
354A VAL 3.5 7.9 - - - +
355A SER* 4.2 13.5 - - - -
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Residues in contact with VAL 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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321A LYS* 4.3 12.8 - - + -
322A GLU 3.7 22.7 - - - +
323A THR* 4.1 9.0 - - + -
344A LEU* 5.8 0.4 - - + -
345A GLU 3.6 7.6 - - - +
346A PRO* 1.3 75.0 - - - +
348A PHE* 1.3 81.4 + - - +
349A ILE* 4.5 3.8 - - + -
353A GLU* 3.3 7.5 - - - +
354A VAL* 2.8 49.3 + - + +
378A VAL* 4.3 20.9 - - + -
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Residues in contact with PHE 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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321A LYS* 3.3 24.1 - - - +
346A PRO* 5.0 3.8 - - + -
347A VAL* 1.3 92.7 - - - +
349A ILE* 1.3 68.4 + - - +
350A GLU 4.2 0.7 - - - -
351A GLY* 3.4 36.6 - - - +
352A SER 3.9 0.9 - - - -
353A GLU* 3.5 34.1 - - + -
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Residues in contact with ILE 349 (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 GLU* 3.2 33.0 - - + +
321A LYS* 4.0 15.7 - - + +
347A VAL* 4.4 2.9 + - + -
348A PHE* 1.3 80.5 - - - +
350A GLU* 1.3 61.3 - - - +
352A SER* 2.6 35.3 + - - -
354A VAL* 3.9 25.4 - - + -
378A VAL* 3.7 45.1 - - + +
379A HIS* 4.6 6.1 - - - +
380A LYS* 3.9 24.2 + - + -
386A PRO* 5.2 1.6 - - + -
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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