Contacts of the strand formed by residues 357 - 360 (chain C) in PDB entry 3SRF
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 CYS 357 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44C THR* 4.0 1.8 - - - -
45C GLY* 3.3 15.5 - - - +
47C ILE* 3.7 28.7 - - + -
70C VAL* 5.7 2.0 - - - -
323C VAL 3.3 3.2 + - - +
324C ILE* 3.4 10.6 - - + -
325C CYS 3.0 22.0 + - - -
355C ALA* 4.0 3.1 - - - +
356C ASP* 1.3 83.1 - - - +
358C ILE* 1.3 68.6 + - - +
463C HIS 3.4 25.4 - - - -
464C LEU* 3.5 25.6 - - - -
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Residues in contact with ILE 358 (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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44C THR* 4.1 15.3 - - + -
45C GLY 2.9 10.9 + - - +
46C ILE* 3.6 4.1 - - + -
47C ILE* 2.9 25.4 + - - +
324C ILE* 4.8 0.7 - - - -
325C CYS* 3.4 8.3 - - + -
329C MET* 3.7 24.7 - - + -
347C VAL* 3.7 24.9 - - + +
350C ALA* 3.8 18.2 - - + -
351C VAL* 5.2 2.7 - - + +
355C ALA* 4.6 4.7 - - + -
357C CYS* 1.3 79.9 - - - +
359C MET* 1.3 61.0 + - - +
377C GLN* 3.4 42.1 + - + +
381C ALA* 4.8 6.1 - - + -
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Residues in contact with MET 359 (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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47C ILE* 3.3 29.4 - - + +
72C ARG* 3.5 49.8 - - - +
240C PHE* 4.5 3.1 - - - -
290C MET* 3.8 24.9 - - + +
324C ILE* 4.2 8.1 - - + -
325C CYS 2.9 17.0 + - - +
326C ALA* 3.7 21.8 - - + -
327C THR* 4.2 6.9 + - - +
328C GLN 5.4 0.2 + - - -
329C MET* 3.3 24.8 + - - +
358C ILE* 1.3 75.7 - - - +
360C LEU* 1.3 65.7 + - - +
361C SER* 4.1 12.1 + - - +
363C GLU* 4.9 0.3 - - - +
377C GLN* 3.8 4.2 - - - +
534C PYR 4.2 5.8 - - + +
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Residues in contact with LEU 360 (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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46C ILE* 4.7 1.1 - - + -
47C ILE 2.9 11.0 + - - +
48C CYS* 4.5 5.8 - - - -
49C THR* 2.9 28.9 + - - +
329C MET* 5.1 0.2 - - + -
330C LEU* 4.1 15.3 - - + +
359C MET* 1.3 71.7 - - - +
361C SER* 1.3 60.4 + - - +
363C GLU* 3.4 34.1 - - + +
364C THR* 3.6 29.8 + - + -
373C ALA* 3.7 34.3 - - + +
374C VAL* 3.9 9.4 - - + +
377C GLN* 3.5 29.1 - - + +
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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