Contacts of the strand formed by residues 327 - 333 (chain C) in PDB entry 1SAF
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 TYR 327 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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331A GLN* 3.6 34.5 - - + +
332A ILE 4.3 2.7 - - - -
333A ARG* 4.0 31.9 + - + +
321C LYS* 5.8 3.6 - - - +
324C ASP* 3.4 34.0 + - + +
325C GLY 2.7 29.2 - - - -
326C GLU* 1.3 75.0 - - - +
328C PHE* 1.3 73.7 + - - +
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Residues in contact with PHE 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331A GLN* 3.1 6.8 - - - +
332A ILE 3.1 32.3 + - - +
334A GLY 3.4 15.9 - - - -
335A ARG* 3.2 52.7 - - + -
338A PHE* 3.5 31.0 - + + -
326C GLU* 3.5 32.5 - - + -
327C TYR* 1.3 80.1 - - - +
329C THR* 1.3 76.6 + - - +
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Residues in contact with THR 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A THR* 5.5 6.3 - - - -
330A LEU 3.1 13.0 - - - -
331A GLN* 3.3 23.8 - - - +
332A ILE 4.4 0.2 - - - +
338A PHE* 2.6 30.1 - - - -
328C PHE* 1.3 88.4 - - - +
330C LEU* 1.3 58.5 + - - +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329A THR* 3.1 5.8 - - - +
330A LEU* 2.9 32.4 + - + +
332A ILE* 3.9 13.9 - - + -
338A PHE* 3.7 14.1 - - + -
341A PHE* 4.3 5.8 - - + -
342A ARG* 4.0 39.3 - - + +
345A ASN* 3.8 32.3 - - + +
329C THR* 1.3 78.2 - - - +
331C GLN* 1.3 71.6 + - - +
332C ILE* 3.6 17.7 + - + +
341C PHE* 4.8 5.2 - - + -
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Residues in contact with GLN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A TYR* 3.6 39.4 - - + +
328A PHE 3.2 15.3 - - - +
329A THR* 3.4 18.0 - - - +
345A ASN* 3.9 12.8 + - - +
349A GLU* 5.5 1.0 - - - +
330C LEU* 1.3 83.3 - - - +
332C ILE* 1.3 62.8 + - - +
333C ARG 4.1 1.1 + - - +
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Residues in contact with ILE 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328A PHE* 3.1 33.5 + - - +
330A LEU* 4.0 15.5 - - + -
345A ASN* 4.3 5.8 - - - +
330C LEU* 3.9 18.2 - - + +
331C GLN* 1.3 80.5 - - - +
333C ARG* 1.3 69.3 + - - +
334C GLY 3.7 1.2 + - - +
337C ARG* 4.1 4.9 - - - -
338C PHE* 3.4 45.1 - - + +
341C PHE* 3.3 55.6 - - + -
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Residues in contact with ARG 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321A LYS* 4.6 21.8 - - - +
323A LEU 3.9 10.3 + - - -
324A ASP* 4.5 2.1 - - - +
325A GLY* 3.2 39.7 - - - +
326A GLU 4.1 2.9 - - - -
327A TYR* 3.9 40.7 + - + +
345A ASN* 5.2 1.2 - - - +
349A GLU* 5.1 11.7 + - - +
331C GLN* 4.1 3.2 + - - +
332C ILE* 1.3 75.6 - - - +
334C GLY* 1.3 64.4 + - - +
337C ARG* 3.6 35.4 + - - +
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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