Contacts of the strand formed by residues 332 - 339 (chain A) in PDB entry 1VCN
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 ALA 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A VAL* 5.0 1.0 - - - +
297A PRO* 4.1 5.4 - - - -
299A ARG* 3.9 23.8 - - + -
301A VAL* 5.0 2.2 - - + -
327A GLY* 2.6 44.0 + - - +
328A ILE* 4.9 0.2 - - - +
330A ASN* 2.6 15.4 + - + +
331A ARG* 1.3 73.7 - - - +
333A ARG* 1.3 65.4 + - - +
334A VAL* 4.0 0.2 - - - +
540A VAL* 5.5 1.1 - - + -
544A LEU* 4.0 21.5 - - + -
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Residues in contact with ARG 333 (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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254A HIS* 5.1 10.0 + - - -
294A LEU 4.0 18.4 + - - +
296A HIS* 4.9 3.8 - - - +
297A PRO* 3.5 34.7 - - + +
299A ARG 3.4 9.3 + - - +
300A THR* 3.2 15.6 + - - +
301A VAL* 3.1 25.1 + - - +
332A ALA* 1.3 74.2 - - - +
334A VAL* 1.3 72.1 + - - +
335A GLU* 4.8 9.4 - - + +
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Residues in contact with VAL 334 (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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301A VAL* 3.4 13.2 - - + +
303A ILE* 4.0 29.2 - - + -
323A LEU* 4.0 20.0 - - + +
324A ARG* 5.9 1.1 - - - -
327A GLY* 3.9 25.5 - - - -
332A ALA 4.0 0.9 - - - +
333A ARG* 1.3 83.0 - - - +
335A GLU* 1.3 75.9 + - - +
336A VAL* 4.1 9.3 + - + +
540A VAL* 4.3 18.2 - - + -
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Residues in contact with GLU 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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300A THR* 3.7 21.4 + - - +
301A VAL 3.0 7.2 + - - +
302A LYS* 3.2 41.2 + - + +
303A ILE 3.0 24.1 + - - +
333A ARG* 4.2 10.9 - - - -
334A VAL* 1.3 81.2 - - - +
336A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 336 (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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302A LYS* 5.0 0.9 - - - -
303A ILE* 3.6 13.2 - - + +
305A ILE* 3.4 39.3 - - + -
320A LEU* 4.8 9.6 - - + -
323A LEU* 5.1 6.1 - - + -
334A VAL* 4.1 11.2 + - + +
335A GLU* 1.3 79.9 - - - +
337A LYS* 1.3 62.9 + - - +
338A TRP* 3.4 32.6 + - + +
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Residues in contact with LYS 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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302A LYS* 4.1 22.8 - - + +
303A ILE 3.0 12.1 + - - +
304A ALA* 3.3 8.3 - - + -
305A ILE 3.0 23.9 + - - -
335A GLU 4.2 0.8 - - - -
336A VAL* 1.3 72.3 - - - +
338A TRP* 1.3 70.0 + - - +
339A VAL* 3.4 22.7 + - + +
351A GLU 4.9 1.6 + - - -
352A ALA* 3.4 30.9 + - - +
354A ARG 5.5 2.6 + - - -
356A VAL* 5.9 1.8 - - + -
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Residues in contact with TRP 338 (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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305A ILE* 3.2 47.3 - - + -
307A GLY* 4.2 17.8 - - - +
308A LYS 4.6 13.9 - - - +
313A PRO* 6.2 2.2 - - + -
316A TYR* 3.2 49.1 - + + -
320A LEU* 3.7 27.5 - - + +
336A VAL* 3.4 25.7 + - + +
337A LYS* 1.3 80.8 - - - +
339A VAL* 1.3 63.1 + - - +
340A ASP* 3.7 3.6 + - - +
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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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304A ALA* 3.6 28.0 - - + -
305A ILE 3.0 11.3 + - - +
306A ALA* 3.3 7.1 - - + +
307A GLY 2.7 30.8 + - - -
337A LYS* 3.4 21.3 + - + +
338A TRP* 1.3 70.7 - - - +
340A ASP* 1.3 62.9 + - - +
341A ALA* 3.7 7.8 + - + +
352A ALA* 3.8 23.8 - - + +
353A PHE* 3.7 28.3 - - + -
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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