Contacts of the strand formed by residues 321 - 332 (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 LYS 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318A ALA 4.4 6.1 + - - -
319A GLU* 3.6 23.3 + - - -
320A GLU* 1.3 101.8 + - - +
322A GLU* 1.3 61.0 + - - +
347A VAL* 4.3 16.2 - - + -
348A PHE 3.3 27.8 - - - +
349A ILE* 4.0 12.8 - - + +
350A GLU 5.6 0.2 - - - +
377A LEU* 3.8 7.3 - - - +
378A VAL* 3.0 41.6 + - + +
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Residues in contact with GLU 322 (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* 1.3 76.9 - - - +
323A THR* 1.3 65.3 + - - +
347A VAL* 3.7 12.0 - - - +
375A TRP* 4.6 8.4 - - + -
376A VAL 3.5 6.7 - - - -
377A LEU* 4.2 13.3 - - + +
392A LEU* 3.5 25.9 - - + +
395A ARG* 2.6 32.4 + - - +
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Residues in contact with THR 323 (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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322A GLU* 1.3 78.4 - - - +
324A ARG* 1.3 61.8 + - - +
344A LEU* 4.3 15.9 - - + -
345A GLU* 3.0 35.2 + - - +
347A VAL* 4.1 11.8 - - + +
375A TRP* 3.3 18.2 - - - -
376A VAL* 2.5 55.2 + - + +
378A VAL* 3.9 21.3 - - + -
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Residues in contact with ARG 324 (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* 1.3 83.4 + - - +
325A LEU* 1.3 69.4 + - - +
326A LEU* 3.6 21.8 + - + +
344A LEU* 3.4 4.5 - - - +
345A GLU* 3.0 33.7 + - + +
373A GLY* 3.0 38.0 + - - +
374A ASP 3.6 4.3 - - - +
375A TRP* 4.0 35.4 - - + +
376A VAL* 4.5 2.7 - - - -
397A THR* 5.3 9.8 - - - +
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Residues in contact with LEU 325 (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 0.4 + - - -
324A ARG* 1.3 76.5 - - - +
326A LEU* 1.3 60.4 + - - +
327A ASP 3.3 30.7 - - - +
328A VAL* 4.5 7.2 - - + +
342A GLY* 4.7 3.6 - - - -
343A VAL 4.3 4.3 - - - +
344A LEU* 4.1 19.7 - - + -
359A LEU* 4.6 8.7 - - + -
370A ILE* 3.3 24.2 - - + -
371A ARG 3.1 23.6 - - - +
372A ILE* 2.7 39.5 - - + +
373A GLY* 4.0 1.4 - - - -
374A ASP 2.8 11.4 + - - +
376A VAL* 4.3 11.3 - - + +
388A VAL* 6.0 0.9 - - + -
403A ILE* 4.6 7.9 - - + -
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Residues in contact with LEU 326 (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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324A ARG* 4.0 35.4 - - + +
325A LEU* 1.3 72.4 - - - +
327A ASP* 1.3 65.3 + - + +
343A VAL* 3.0 16.9 + - + +
344A LEU 4.3 4.3 - - - +
345A GLU* 3.7 42.0 - - - +
346A PRO* 5.2 1.8 - - + -
372A ILE* 2.9 25.3 - - - +
373A GLY* 5.9 0.2 - - - -
401A ARG* 4.7 4.0 + - - -
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Residues in contact with ASP 327 (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* 3.3 8.1 - - - +
326A LEU* 1.3 82.6 - - + +
328A VAL* 1.3 83.6 + - - +
329A VAL* 4.2 12.4 - - - +
343A VAL* 2.8 41.9 + - + +
372A ILE* 4.6 8.1 - - - +
401A ARG* 5.1 6.1 + - - +
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Residues in contact with VAL 328 (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* 4.6 3.4 - - + -
327A ASP* 1.3 89.4 + - - +
329A VAL* 1.3 71.9 + - - +
330A PHE* 4.6 16.1 - - + -
340A PRO* 4.8 1.6 - - + -
341A VAL 3.3 18.6 - - - +
342A GLY* 4.4 0.7 - - - -
343A VAL 4.3 0.2 - - - +
359A LEU* 3.6 26.2 - - + -
372A ILE* 3.8 27.4 - - + -
403A ILE* 4.2 26.5 - - + -
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Residues in contact with VAL 329 (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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327A ASP* 4.2 13.2 - - - +
328A VAL* 1.3 80.3 - - - +
330A PHE* 1.3 69.8 + - - +
331A GLN* 4.9 4.7 - - + +
341A VAL* 2.8 53.1 + - + +
343A VAL* 4.0 15.5 - - + -
356A ARG* 3.9 31.9 - - - +
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Residues in contact with PHE 330 (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* 4.6 14.6 - - + -
329A VAL* 1.3 79.9 - - - +
331A GLN* 1.3 69.2 + - - +
338A VAL* 4.0 12.1 - - + -
339A THR 3.3 16.4 - - - +
340A PRO* 3.8 13.5 - - + -
403A ILE* 4.1 12.3 - - + -
404A ARG 3.4 26.7 - - - -
405A TRP* 3.5 47.3 - + - -
406A PRO* 3.5 26.0 - - + -
410A PRO* 4.4 15.5 - - + +
411A GLU* 5.7 0.2 - - - +
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Residues in contact with GLN 331 (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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329A VAL* 4.9 3.3 - - + +
330A PHE* 1.3 79.6 - - - +
332A VAL* 1.3 59.7 + - - +
333A GLY 4.2 0.2 - - - -
338A VAL* 3.1 9.6 - - - +
339A THR* 2.6 47.9 + - - +
341A VAL* 3.7 29.2 - - + +
356A ARG* 4.5 12.8 + - - -
410A PRO* 5.2 4.3 - - - -
411A GLU* 5.3 5.4 - - - +
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Residues in contact with VAL 332 (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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331A GLN* 1.3 79.1 - - - +
333A GLY* 1.3 74.5 + - - +
336A GLY* 3.4 27.1 - - - +
337A ARG 3.6 2.9 - - - -
338A VAL* 4.2 9.6 - - + +
409A CYS* 4.8 7.4 - - - -
410A PRO* 5.3 2.0 - - + -
411A GLU* 3.2 40.0 + - + +
425A CYS* 5.0 1.6 - - + -
430A CYS* 4.7 6.7 - - - -
432A ALA* 3.3 24.2 - - + +
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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