Contacts of the helix formed by residues 316 - 321 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461B GLU* 2.6 35.5 + - - +
465B TYR* 3.4 15.1 + - - +
315H THR* 1.3 73.2 - - - +
317H ASN* 1.3 62.0 + - - +
319H TYR* 3.3 24.5 + - - +
320H LYS* 3.7 11.2 + - - -
414H LEU* 4.0 10.3 - - + +
450H ASP* 3.2 36.6 - - - +
453H VAL* 3.5 21.1 - - + +
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Residues in contact with ASN 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457B PRO* 4.1 4.8 - - - +
461B GLU* 2.9 32.7 + - + +
465B TYR* 4.1 13.0 - - + -
256H MET* 3.5 18.7 - - + +
257H PRO* 3.2 13.2 - - + +
258H LYS* 2.7 53.0 + - - +
315H THR* 3.0 8.5 - - - +
316H THR* 1.3 80.8 + - - +
318H SER* 1.3 65.5 + - - +
320H LYS* 2.9 22.3 + - - +
321H ARG 3.8 2.3 + - - -
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Residues in contact with SER 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257H PRO* 3.6 8.3 - - - +
313H ASN* 3.6 21.0 - - - -
315H THR* 2.6 41.7 + - - -
317H ASN* 1.3 77.7 - - - +
319H TYR* 1.3 59.2 + - - +
321H ARG* 3.2 19.2 + - - +
322H LEU* 3.3 16.3 + - - +
362H ASP* 2.7 33.4 + - - +
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Residues in contact with TYR 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454B ARG* 4.7 9.1 + - - +
309H ASN* 3.6 8.7 + - + +
313H ASN* 2.8 26.9 + - + +
315H THR 3.2 23.1 - - - -
316H THR* 3.6 9.9 - - - +
317H ASN 3.1 1.0 - - - -
318H SER* 1.3 73.5 - - - +
320H LYS* 1.3 61.4 + - - +
321H ARG 3.3 1.3 - - - -
322H LEU* 3.4 40.3 - - + +
323H VAL* 4.2 8.0 - - - +
411H ALA* 3.5 30.5 - - + -
412H GLY 4.0 13.4 - - - +
413H SER* 3.7 19.7 - - - -
414H LEU* 3.3 28.0 - - + -
417H ALA* 3.3 21.7 - - - +
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Residues in contact with LYS 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453B VAL 4.1 4.4 + - - -
454B ARG* 3.1 29.9 + - - +
455B MET* 3.8 13.9 - - - +
456B THR 3.2 22.9 - - - +
457B PRO* 3.7 14.1 - - + -
458B HIS* 4.4 3.3 - - - +
461B GLU* 2.7 41.1 + - - +
258H LYS* 3.4 29.1 - - + -
316H THR* 3.7 10.4 + - - +
317H ASN* 2.9 13.4 + - - +
319H TYR* 1.3 79.6 - - - +
321H ARG* 1.3 59.6 + - - +
323H VAL* 4.0 15.4 - - - +
453H VAL* 5.0 5.5 - - - +
458H HIS* 5.2 0.4 - - - -
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Residues in contact with ARG 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257H PRO* 4.1 20.6 - - + +
258H LYS* 4.1 12.6 + - + +
265H GLY* 4.4 9.4 + - - +
266H SER 3.4 26.0 + - - +
267H GLY* 3.4 24.6 - - - +
269H HIS* 4.5 7.3 + - - -
313H ASN* 4.1 1.8 + - - -
317H ASN 3.8 1.2 + - - -
318H SER 3.2 10.7 + - - +
320H LYS* 1.3 78.7 - - - +
322H LEU* 1.3 70.6 + - + +
323H VAL* 2.9 14.8 + - - +
328H ALA* 4.0 12.5 - - - +
329H PRO* 4.2 13.5 - - + +
359H ARG 3.3 22.0 + - - -
360H PHE 2.9 26.1 + - - -
361H PRO 3.5 5.5 + - - -
362H ASP* 3.9 6.7 + - - +
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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