Contacts of the strand formed by residues 361 - 366 (chain L) in PDB entry 1VYH
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 THR 361 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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337L HIS* 3.4 31.4 + - + +
356L CYS* 3.4 20.3 - - - +
357L ALA 3.4 6.9 + - - -
359L ASP* 2.0 53.3 + - - +
360L LYS 1.3 67.4 - - - -
362L LEU* 1.3 64.5 + - - +
363L ARG* 3.6 7.9 + - + +
375L THR* 3.7 8.4 - - + +
376L LEU 3.5 14.8 + - - +
377L ASN* 4.4 8.3 + - - -
383L VAL* 3.5 7.7 - - - +
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Residues in contact with LEU 362 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L PRO 5.1 3.8 - - - +
354L LEU* 4.8 8.1 - - + -
355L SER 2.6 33.0 - - - +
356L CYS* 4.1 10.3 - - + +
361L THR* 1.3 72.9 - - - +
363L ARG* 1.3 60.2 + - - +
364L VAL* 4.0 7.8 + - + +
375L THR* 4.0 0.2 - - - -
376L LEU* 2.9 62.6 + - + +
378L ALA* 4.2 11.7 - - + +
383L VAL* 5.5 0.9 - - + -
386L LEU* 4.2 19.1 - - + -
395L VAL* 4.7 18.4 - - + -
397L THR* 4.9 10.8 - - - +
407L TRP* 4.9 12.1 - - + +
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Residues in contact with ARG 363 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318L LYS 4.5 2.2 + - - -
320L ILE* 4.6 3.8 - - - +
336L GLY* 3.7 6.2 - - - -
337L HIS* 3.0 75.5 + - + +
339L ASN 4.0 9.1 + - - -
341L VAL* 3.4 26.1 - - - +
354L LEU* 3.5 1.7 - - - +
355L SER* 2.8 65.8 + - - +
356L CYS 4.2 1.1 - - - +
357L ALA* 3.8 9.6 - - - +
359L ASP* 3.3 23.5 + - - -
361L THR* 3.6 11.0 - - + +
362L LEU* 1.3 72.1 - - - +
364L VAL* 1.3 60.8 + - - +
365L TRP* 3.6 14.8 - - - +
372L CYS* 4.2 3.8 - - - -
374L LYS 3.9 5.6 - - - -
375L THR* 4.5 0.2 - - - +
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Residues in contact with VAL 364 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96L PRO* 3.9 35.2 - - + +
352L PHE* 4.3 15.9 - - + -
354L LEU* 3.3 31.2 - - + -
362L LEU* 4.6 10.3 - - + +
363L ARG* 1.3 72.1 - - - +
365L TRP* 1.3 62.0 + - - +
372L CYS* 3.9 1.2 - - - -
373L MET* 3.0 36.4 + - - +
374L LYS* 3.4 31.8 + - + -
376L LEU* 5.6 1.8 - - + -
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Residues in contact with TRP 365 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L ILE* 3.8 13.4 - - + +
334L LEU* 3.4 45.5 - - + -
335L VAL 3.4 10.8 - - - -
336L GLY* 3.0 42.6 - - - -
337L HIS* 4.5 4.5 - + - -
352L PHE* 3.2 30.5 - - - +
353L ILE* 2.7 37.6 + - + +
355L SER* 3.5 24.4 - - - -
363L ARG* 3.6 17.8 - - - +
364L VAL* 1.3 73.1 - - - +
366L ASP* 1.3 62.3 + - - +
367L TYR 4.0 1.3 + - - +
370L LYS 5.4 3.4 - - - -
371L ARG 4.0 7.0 - - - -
372L CYS* 3.9 39.3 - - + -
373L MET* 4.3 1.1 - - - +
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Residues in contact with ASP 366 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138H GLU* 4.7 6.4 - - - +
334L LEU* 5.3 0.7 - - - +
351L LYS 4.1 6.9 - - - +
352L PHE* 4.2 15.6 - - + -
365L TRP* 1.3 74.7 - - - +
367L TYR* 1.3 59.4 + - - +
368L LYS* 2.5 66.6 + - - +
369L ASN* 4.1 3.4 + - - -
370L LYS* 3.2 1.9 + - - -
371L ARG* 2.9 40.3 + - + +
373L MET* 3.9 17.5 - - + +
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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