Contacts of the helix formed by residues 316 - 321 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B THR* 1.3 74.8 - - - +
317B ASN* 1.3 61.2 + - - +
319B TYR* 3.3 24.6 + - - +
320B LYS* 3.7 10.9 + - - -
414B LEU* 4.0 11.6 - - + +
450B ASP* 3.2 35.9 - - - +
453B VAL* 3.5 21.4 - - + +
461H GLU* 2.6 35.3 + - - +
465H TYR* 3.4 16.2 + - - +
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Residues in contact with ASN 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256B MET* 3.5 18.1 - - + +
257B PRO* 3.2 13.3 - - + +
258B LYS* 2.7 52.3 + - - +
315B THR* 3.6 8.0 - - - +
316B THR* 1.3 78.9 + - - +
318B SER* 1.3 64.8 + - - +
320B LYS* 2.9 21.9 + - - +
321B ARG 3.8 2.4 + - - -
457H PRO* 4.1 5.9 - - - +
461H GLU* 2.9 31.4 + - + +
465H TYR* 4.1 13.4 - - + -
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Residues in contact with SER 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B PRO* 3.6 8.4 - - - +
313B ASN* 3.6 21.6 - - - -
314B PRO 3.9 0.2 - - - -
315B THR* 2.6 41.7 + - - +
317B ASN* 1.3 77.6 - - - +
319B TYR* 1.3 57.7 + - - +
321B ARG* 3.2 19.2 + - - +
322B LEU* 3.3 16.2 + - - +
362B ASP* 2.7 32.7 + - - +
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Residues in contact with TYR 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B ASN* 3.6 8.9 + - + +
313B ASN* 2.8 27.8 + - + +
315B THR 3.2 20.9 - - - -
316B THR* 3.6 10.1 - - - +
317B ASN 3.1 1.0 - - - -
318B SER* 1.3 74.3 - - - +
320B LYS* 1.3 61.5 + - + +
321B ARG 3.3 1.3 - - - -
322B LEU* 3.4 39.3 - - + +
323B VAL* 4.2 7.8 - - - +
411B ALA* 3.5 30.3 - - + -
412B GLY 4.0 13.3 - - - +
413B SER* 3.7 20.2 - - - -
414B LEU* 3.3 28.7 - - + -
417B ALA* 3.3 21.7 - - - +
454H ARG* 4.7 9.2 + - - +
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Residues in contact with LYS 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LYS* 3.4 29.9 - - + -
316B THR* 3.7 10.6 + - - +
317B ASN* 2.9 13.6 + - - +
319B TYR* 1.3 78.5 - - + +
321B ARG* 1.3 59.9 + - - +
323B VAL* 4.0 16.6 - - - +
453B VAL* 5.0 5.7 - - - +
458B HIS* 5.2 0.4 - - - -
453H VAL 4.1 4.2 + - - -
454H ARG* 3.1 30.2 + - - +
455H MET* 3.8 13.1 - - - +
456H THR 3.2 23.6 - - - +
457H PRO* 3.6 14.4 - - + -
458H HIS* 4.3 3.5 - - - +
461H GLU* 2.7 40.8 + - - +
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B PRO* 4.1 20.4 - - + +
258B LYS* 4.1 14.4 + - + +
265B GLY* 4.4 9.4 - - - +
266B SER 3.4 25.5 + - - +
267B GLY* 3.4 24.1 - - - +
269B HIS* 4.5 7.1 + - - -
313B ASN* 4.1 1.8 + - - -
317B ASN 3.8 1.4 + - - -
318B SER 3.2 11.0 + - - +
320B LYS* 1.3 78.4 - - - +
322B LEU* 1.3 70.9 + - + +
323B VAL* 2.9 14.6 + - - +
328B ALA* 4.0 12.8 - - - +
329B PRO* 4.2 14.1 - - + +
359B ARG 3.3 22.2 + - - -
360B PHE 2.9 25.5 + - - -
361B PRO 3.5 5.3 + - - -
362B ASP* 3.9 7.7 + - - +
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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