Contacts of the strand formed by residues 331 - 335 (chain G) in PDB entry 1F1H
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328G ALA 5.6 0.2 - - - +
330G VAL* 1.3 84.8 - - + +
332G LEU* 1.3 56.2 + - - +
333G ALA* 2.9 11.9 + - + +
340G SER* 3.4 29.7 + - - +
341G ALA* 3.9 2.1 - - - -
342G SER* 2.5 31.0 + - - -
392G MET* 5.8 7.6 - - + -
396G LEU* 4.8 3.6 - - - -
397G TYR* 3.9 44.4 - - + +
405G LYS* 5.2 4.5 - - + -
407G ILE* 4.0 31.6 - - + -
408G PRO 3.9 2.9 - - - -
409G GLN* 3.9 26.5 - - - +
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Residues in contact with LEU 332 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G ILE* 3.6 43.2 - - + +
305G ALA* 3.6 29.6 - - + -
306G LYS* 5.3 3.6 - - + +
331G MET* 1.3 65.8 - - - +
333G ALA* 1.3 60.6 + - - +
342G SER* 3.7 10.3 - - - +
343G ILE* 6.0 0.4 - - - -
360G PHE* 5.0 3.4 - - + -
407G ILE* 4.4 5.9 - - - +
408G PRO* 2.8 35.5 + - + +
409G GLN 3.4 22.7 - - - +
410G VAL* 3.5 34.3 - - + +
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Residues in contact with ALA 333 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302G ILE* 4.1 9.8 - - - +
331G MET* 2.9 10.4 + - + +
332G LEU* 1.3 75.8 - - - +
334G TYR* 1.3 62.3 + - - +
341G ALA* 3.5 10.9 - - + +
342G SER* 3.7 0.7 + - - -
343G ILE* 3.4 25.6 + - - +
390G GLU 5.5 1.3 - - - +
392G MET* 3.6 43.1 - - + +
407G ILE* 4.7 7.2 - - + -
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Residues in contact with TYR 334 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G TYR* 4.4 16.4 - + - +
295G LEU* 4.0 20.2 - - + +
298G ILE* 4.1 36.1 - - + -
302G ILE* 4.7 2.2 - - + -
333G ALA* 1.3 77.6 - - - +
335G SER* 1.3 62.2 + - - +
341G ALA* 4.4 0.7 - - - -
343G ILE* 3.3 15.5 - - + +
345G ILE* 4.4 6.7 - - + -
387G HIS* 4.7 2.3 - - - -
388G PRO* 3.3 41.9 - - + +
389G GLY 2.6 20.5 + - - -
390G GLU* 3.9 8.5 - - - -
391G PRO* 3.2 38.6 - - + +
392G MET 2.9 24.9 + - - -
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Residues in contact with SER 335 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287G TYR* 3.9 8.3 - - - -
334G TYR* 1.3 79.8 - - - +
336G ALA* 1.3 63.9 + - - +
337G ARG* 3.1 4.9 + - - +
338G ASN* 2.9 31.9 + - - +
341G ALA* 4.0 8.5 - - - +
343G ILE 3.1 5.9 + - - +
344G ARG* 3.2 10.9 - - - +
345G ILE* 2.9 25.5 + - - +
392G MET 3.7 16.4 - - - -
393G ASP* 3.6 11.5 + - - -
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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