Contacts of the strand formed by residues 331 - 335 (chain C) in PDB entry 1FPY
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 MET 331 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330C VAL* 1.3 89.1 - - + +
332C LEU* 1.3 55.0 + - - +
333C ALA* 2.9 6.2 + - + +
340C SER* 3.4 26.2 + - - +
341C ALA* 3.8 2.6 - - - -
342C SER* 2.4 37.1 + - - -
392C MET* 6.2 0.4 - - + -
396C LEU 5.7 1.3 - - - +
397C TYR* 5.1 11.7 - - + +
400C PRO* 5.7 10.1 - - + -
405C LYS* 5.3 7.2 - - + +
407C ILE* 3.9 29.8 - - + -
408C PRO 4.0 0.2 - - - -
409C GLN* 3.5 35.7 - - - +
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Residues in contact with LEU 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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301C VAL* 6.4 0.4 - - + -
302C ILE* 3.6 32.6 - - + +
305C ALA* 3.4 31.6 - - + -
306C LYS* 5.7 0.9 - - + -
330C VAL 3.4 1.8 + - - -
331C MET* 1.3 66.8 - - - +
333C ALA* 1.3 59.9 + - - +
342C SER* 3.4 15.7 - - - +
343C ILE* 4.5 5.8 - - + -
360C PHE* 4.5 8.5 - - + -
407C ILE* 5.0 1.7 - - - +
408C PRO* 2.9 40.9 + - + +
409C GLN* 3.1 36.6 - - - +
410C VAL* 3.4 20.9 - - + +
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Residues in contact with ALA 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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302C ILE* 4.3 5.4 - - - -
331C MET* 2.9 9.5 + - + +
332C LEU* 1.3 74.8 - - - +
334C TYR* 1.3 63.2 + - + +
341C ALA* 3.5 11.0 - - + +
342C SER* 3.8 0.4 + - - -
343C ILE* 3.0 31.6 + - - +
390C GLU 5.8 0.9 - - - +
392C MET* 3.3 35.7 - - + -
407C ILE* 4.3 11.2 - - + -
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Residues in contact with TYR 334 (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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287C TYR* 4.5 7.8 - + - +
290C LEU* 5.1 0.9 - - + -
295C LEU* 3.5 32.6 - - + +
298C ILE* 3.9 27.8 - - + -
302C ILE* 4.7 1.6 - - + -
333C ALA* 1.3 79.6 - - - +
335C SER* 1.3 63.8 + - - +
341C ALA* 4.2 1.3 - - - -
343C ILE* 3.2 25.4 - - + +
345C ILE* 4.3 11.7 - - + -
387C HIS* 5.1 0.5 - - - -
388C PRO* 3.3 29.8 - - + -
389C GLY 2.5 22.3 + - - -
390C GLU 3.9 2.9 - - - -
391C PRO* 3.2 43.1 - - + +
392C MET* 2.9 25.8 + - - -
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Residues in contact with SER 335 (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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287C TYR* 3.8 11.4 - - - -
334C TYR* 1.3 75.9 - - - +
336C ALA* 1.3 58.4 + - - +
337C ARG 2.9 12.5 + - - -
338C ASN* 3.1 21.1 + - - -
341C ALA* 4.4 4.0 - - - -
343C ILE 3.3 4.4 + - - -
344C ARG* 3.2 10.8 - - - +
345C ILE* 2.7 31.1 + - - +
392C MET 2.8 29.7 + - - -
393C ASP* 3.2 6.9 + - - -
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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