Contacts of the strand formed by residues 328 - 334 (chain A) in PDB entry 1MF8
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 VAL 328 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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323A LYS 2.9 14.6 - - - +
324A TYR* 3.8 4.7 - - - -
325A GLU* 2.5 29.4 + - - +
326A ASN* 3.3 15.5 - - + +
327A ASN* 1.3 78.6 - - - +
329A MET* 1.3 67.7 + - - +
330A ASN* 3.3 13.0 + - + +
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Residues in contact with MET 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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191A MET* 4.1 1.6 - - + -
195A PHE* 3.8 26.0 - - + -
278A LEU* 3.5 32.5 - - + -
299A PHE* 4.3 16.8 - - + -
303A ILE* 4.3 7.0 - - + -
322A LEU* 2.7 58.8 - - + -
323A LYS 3.4 4.5 - - - -
324A TYR* 3.8 18.8 - - + +
327A ASN 4.2 0.6 - - - -
328A VAL* 1.3 72.8 - - - +
330A ASN* 1.3 61.1 + - - +
331A ILE* 3.8 9.5 + - + +
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Residues in contact with ASN 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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322A LEU* 4.7 0.4 - - - -
323A LYS* 2.6 57.5 + - + +
328A VAL* 3.3 14.8 + - + +
329A MET* 1.3 73.5 - - - +
331A ILE* 1.3 69.9 + - - +
332A ARG* 3.4 25.1 + - - +
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Residues in contact with ILE 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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288A TYR* 3.3 52.7 - - + +
290A MET* 3.2 40.6 - - + -
303A ILE* 6.0 0.9 - - + -
305A ILE* 6.3 0.2 - - + -
320A ALA* 4.1 10.5 - - + -
321A VAL 3.7 9.4 - - - +
322A LEU* 4.6 13.2 - - + +
329A MET* 3.8 7.8 + - + +
330A ASN* 1.3 82.4 + - - +
332A ARG* 1.3 60.5 + - - +
333A GLN* 3.8 7.3 + - + +
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Residues in contact with ARG 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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104A VAL* 3.5 41.2 + - + +
320A ALA* 2.9 26.2 - - - +
321A VAL* 2.9 31.3 + - + +
323A LYS* 3.7 32.3 - - + +
330A ASN* 3.4 15.9 + - - +
331A ILE* 1.3 73.0 - - - +
333A GLN* 1.3 71.3 + - - +
334A PHE* 4.5 0.7 - - - -
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Residues in contact with GLN 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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104A VAL* 5.5 0.2 - - - -
286A ALA* 2.5 45.2 + - - +
288A TYR* 3.7 13.3 - - - -
318A LYS* 4.5 21.5 + - + +
319A ALA 3.1 6.7 - - - +
320A ALA* 4.0 5.2 - - + -
331A ILE* 3.8 11.3 + - + +
332A ARG* 1.3 91.6 + - - +
334A PHE* 1.3 64.7 + - - +
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Residues in contact with PHE 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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97A ASP 3.2 25.6 - - - -
100A LYS* 3.7 26.2 - - + -
101A LEU* 3.7 27.4 - - + -
104A VAL* 4.1 22.2 - - + -
307A SER* 4.0 12.8 - - - -
309A PRO* 4.3 4.9 - - + -
318A LYS* 3.7 3.8 - - - +
319A ALA* 2.7 66.1 + - + +
320A ALA* 3.1 21.1 - - - -
321A VAL* 4.4 5.6 - - + -
332A ARG 4.5 1.6 - - - -
333A GLN* 1.3 77.4 - - - +
335A ASN* 1.3 72.8 + - - +
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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