Contacts of the strand formed by residues 327 - 331 (chain A) in PDB entry 5VFC
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 ILE 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A THR* 3.4 3.6 - - - +
41A LEU* 2.7 45.1 + - + +
44A HIS* 4.2 9.2 - - + -
48A VAL* 4.2 5.4 - - + -
51A VAL* 3.8 17.7 - - + -
60A LEU* 3.6 25.8 - - + -
62A SER* 3.5 32.1 - - - +
72A TRP* 3.7 26.0 - - + +
317A ALA* 4.5 2.2 - - + -
318A SER 3.1 12.3 - - - +
319A ALA* 4.1 5.8 - - + -
326A THR* 1.3 77.8 - - - +
328A LYS* 1.3 69.6 + - - +
329A LEU* 5.0 0.2 - - + -
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Residues in contact with LYS 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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37A LEU* 3.6 20.2 - - + +
39A PHE 3.4 2.2 - - - -
40A THR* 3.0 37.7 + - + +
299A GLY* 3.7 29.6 + - - -
300A HIS* 3.7 25.5 - - + +
317A ALA* 3.3 6.2 - - - +
318A SER* 2.8 34.8 + - - +
324A ASP* 4.7 0.9 - - - -
326A THR* 4.1 6.7 + - - -
327A ILE* 1.3 79.7 - - - +
329A LEU* 1.4 62.6 + - - +
330A TRP* 3.5 35.1 - - + +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 3.6 3.3 - - - +
38A LYS* 2.8 32.3 + - - -
39A PHE* 2.9 21.9 + - + +
41A LEU* 4.3 13.7 - - + -
53A PHE* 3.9 18.6 - - + -
60A LEU* 4.1 11.9 - - + -
73A GLY 4.1 3.4 - - - +
74A ALA* 3.7 10.5 - - - +
77A GLY* 3.8 28.3 - - - +
315A ILE* 4.5 1.6 - - + -
316A ILE 3.5 2.0 - - - +
317A ALA* 3.7 27.8 - - + -
328A LYS* 1.4 73.9 - - - +
330A TRP* 1.3 55.7 + - - +
408A EDO 3.4 28.9 - - - +
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Residues in contact with TRP 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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35A TYR* 3.7 19.9 - - + -
36A ALA* 3.2 11.9 - - - +
37A LEU* 3.5 40.4 - - + -
38A LYS* 4.5 0.9 - - - -
283A VAL* 4.5 1.8 - - + +
297A LEU* 3.6 41.6 - - + +
298A GLN 3.3 28.9 - - - -
299A GLY* 4.7 0.9 - - - -
300A HIS* 4.5 6.5 - + - -
315A ILE* 3.2 8.8 - - - +
316A ILE* 3.0 51.7 + - + +
318A SER* 2.8 25.5 + - - -
328A LYS* 3.5 34.5 - - + +
329A LEU* 1.3 71.7 - - - +
331A LYS* 1.3 60.8 + - - +
408A EDO 5.1 0.2 - - - -
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Residues in contact with LYS 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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34A ASN 3.6 2.4 - - - +
35A TYR* 3.3 3.3 - - - -
36A ALA* 2.9 31.2 + - - +
38A LYS* 3.9 27.5 - - + +
313A GLU* 6.0 0.7 - - + -
314A ASN 3.3 13.9 - - - +
315A ILE* 3.9 13.7 - - + -
330A TRP* 1.3 74.4 - - - +
332A SER* 1.3 68.2 + - - +
408A EDO 4.2 12.6 - - - -
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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