Contacts of the strand formed by residues 390 - 398 (chain A) in PDB entry 2XVS
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 ASN 390 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A GLY* 3.3 25.0 - - - -
331A VAL* 3.7 21.1 + - + +
388A GLU 3.5 2.3 + - - +
389A PRO* 1.3 71.0 - - - +
391A LEU* 1.3 63.5 + - - +
392A ARG* 3.8 5.8 + - - +
407A SER 3.7 0.2 - - - +
408A VAL* 3.3 7.2 - - - +
409A ARG* 2.8 70.2 + - - +
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Residues in contact with LEU 391 (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 LEU* 3.7 37.5 - - + +
328A GLN 3.5 19.1 - - - +
329A PRO* 3.6 4.8 - - + +
330A GLY* 2.7 36.4 + - - +
332A ASN* 4.1 5.2 - - - +
365A TYR* 4.5 16.2 - - + -
389A PRO 3.6 0.6 + - - -
390A ASN* 1.3 73.5 - - - +
392A ARG* 1.3 62.7 + - - +
393A LEU* 3.6 24.7 - - + -
406A SER* 3.9 20.4 - - - +
407A SER 3.5 12.8 - - - +
408A VAL* 3.9 18.2 - - + +
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Residues in contact with ARG 392 (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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368A MET* 3.3 20.6 - - - +
370A TYR* 3.2 30.3 + - - -
390A ASN* 4.6 7.0 - - - +
391A LEU* 1.3 78.0 - - - +
393A LEU* 1.3 61.4 + - - +
394A HIS* 3.6 26.7 + - + +
406A SER* 3.2 8.1 - - - -
407A SER* 2.8 55.2 + - - +
409A ARG* 3.7 41.9 - - + +
1428A IOD 4.4 14.6 - - + -
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Residues in contact with LEU 393 (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 PRO* 3.8 34.5 - - + +
391A LEU* 3.6 32.3 + - + -
392A ARG* 1.3 74.5 - - - +
394A HIS* 1.3 63.5 + - - +
395A ARG* 3.6 29.1 + - + +
405A PHE 4.0 3.1 - - - -
406A SER* 3.9 12.1 - - - +
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Residues in contact with HIS 394 (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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368A MET* 4.9 2.8 - - + -
392A ARG* 3.6 36.8 + - + +
393A LEU* 1.3 71.1 - - - +
395A ARG* 1.3 63.4 + - - +
396A ILE* 4.0 15.5 - - + +
404A SER* 3.3 5.9 + - - -
405A PHE* 2.8 78.1 + + + +
407A SER* 2.7 34.4 + - - -
1428A IOD 3.9 14.2 - - + +
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Residues in contact with ARG 395 (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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393A LEU* 3.6 35.2 + - - +
394A HIS* 1.3 79.2 - - - +
396A ILE* 1.3 60.7 + - - +
397A GLN* 4.2 2.0 + - - -
402A ASP* 5.5 0.7 - - - +
403A TYR 3.5 6.3 - - - -
404A SER* 4.6 12.6 - - - +
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Residues in contact with ILE 396 (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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267A LEU* 6.2 1.1 - - + -
268A LEU* 5.5 1.6 - - + -
271A LEU* 3.9 26.5 - - + -
394A HIS* 4.1 18.8 - - + +
395A ARG* 1.3 76.3 - - - +
397A GLN* 1.3 64.4 + - - +
398A HIS* 4.3 19.5 - - + +
401A LYS 3.8 0.3 - - - +
402A ASP* 3.3 6.2 - - - +
403A TYR* 2.9 52.8 + - + +
405A PHE* 4.0 23.3 - - + -
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Residues in contact with GLN 397 (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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395A ARG 4.2 2.5 + - - -
396A ILE* 1.3 72.0 - - - +
398A HIS* 1.3 62.9 + - - +
401A LYS 3.3 7.0 - - - +
402A ASP* 3.1 37.0 + - + +
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Residues in contact with HIS 398 (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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264A GLU* 2.7 35.1 + - + +
267A LEU* 6.3 1.1 - - + -
268A LEU* 4.2 22.7 - - + +
396A ILE* 4.1 16.0 - - + +
397A GLN* 1.3 76.0 + - - +
399A LYS* 1.3 96.0 + - + +
400A GLY 3.3 2.0 - - - +
401A LYS* 3.0 26.9 + - - +
403A TYR* 5.9 0.2 - - - -
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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