Contacts of the helix formed by residues 316 - 321 (chain A) 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 THR 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A THR* 1.3 73.7 - - - +
317A ASN* 1.3 61.6 + - - +
319A TYR* 3.3 24.9 + - - +
320A LYS* 3.7 10.5 + - - -
414A LEU* 4.0 11.2 - - + +
450A ASP* 3.2 35.9 - - - +
453A VAL* 3.5 22.4 - - + +
461G GLU* 2.7 34.9 + - - +
465G TYR* 3.3 15.3 + - - +
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Residues in contact with ASN 317 (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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256A MET* 3.5 18.5 - - - +
257A PRO* 3.2 13.8 - - + +
258A LYS* 2.7 53.6 + - - +
315A THR* 3.6 7.9 - - - +
316A THR* 1.3 79.7 + - - +
318A SER* 1.3 64.1 + - - +
320A LYS* 2.9 21.0 + - - +
321A ARG 3.8 2.6 + - - -
457G PRO* 4.2 4.8 - - - +
461G GLU* 2.8 32.6 + - - +
465G TYR* 4.0 13.9 - - + -
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A PRO* 3.6 8.2 - - - +
313A ASN* 3.6 20.8 - - - -
314A PRO 3.9 0.2 - - - -
315A THR* 2.6 41.4 + - - -
317A ASN* 1.3 78.0 - - - +
319A TYR* 1.3 56.8 + - - +
321A ARG* 3.2 19.9 + - - +
322A LEU* 3.3 15.8 + - - +
362A ASP* 2.7 34.0 + - - +
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Residues in contact with TYR 319 (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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309A ASN* 3.6 9.0 + - + +
313A ASN* 2.8 26.8 + - + +
315A THR 3.2 21.8 - - - -
316A THR* 3.6 10.8 - - - +
317A ASN 3.1 0.8 - - - -
318A SER* 1.3 73.3 - - - +
320A LYS* 1.3 61.2 + - + +
321A ARG 3.3 1.6 - - - -
322A LEU* 3.4 40.5 - - + +
323A VAL* 4.2 8.0 - - - +
411A ALA* 3.5 30.7 - - + -
412A GLY* 4.0 13.8 - - - +
413A SER* 3.7 19.3 - - - -
414A LEU* 3.3 28.5 - - + -
417A ALA* 3.3 21.7 - - - +
454G ARG* 4.6 9.0 + - - +
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Residues in contact with LYS 320 (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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258A LYS* 3.4 29.4 - - + -
316A THR* 3.7 10.6 + - - +
317A ASN* 2.9 12.8 + - - +
319A TYR* 1.3 78.8 - - - +
321A ARG* 1.3 60.4 + - - +
323A VAL* 4.0 17.0 - - - +
453A VAL* 5.0 6.1 - - - +
458A HIS* 5.2 0.2 - - - -
453G VAL 4.1 6.8 + - - -
454G ARG* 3.1 28.4 + - - +
455G MET* 3.9 12.9 - - - +
456G THR 3.2 23.1 - - - +
457G PRO* 3.6 14.4 - - + -
458G HIS* 4.3 4.4 - - - +
461G GLU* 2.7 41.1 + - - +
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Residues in contact with ARG 321 (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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257A PRO* 4.1 20.4 - - + +
258A LYS* 4.1 14.0 + - + +
265A GLY* 4.5 9.6 - - - +
266A SER 3.4 26.0 + - - +
267A GLY* 3.4 24.1 - - - +
269A HIS* 4.5 6.9 + - - -
313A ASN* 4.1 1.4 + - - -
317A ASN 3.8 1.2 + - - -
318A SER 3.2 10.9 + - - +
320A LYS* 1.3 79.3 - - - +
322A LEU* 1.3 71.6 + - + +
323A VAL* 2.9 14.8 + - - +
328A ALA* 4.0 12.6 - - - +
329A PRO* 4.2 13.3 - - + +
359A ARG 3.3 22.8 + - - -
360A PHE 2.9 25.7 + - - -
361A PRO 3.5 5.3 + - - -
362A ASP* 3.9 7.4 + - - +
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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