Contacts of the helix formed by residues 304 - 313 (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 HIS 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300A GLY* 3.0 24.0 + - - +
301A VAL 3.6 1.8 - - - -
303A LYS* 1.3 100.7 + - + +
305A ALA* 1.3 65.1 + - - +
306A LYS 3.4 2.5 - - - -
307A ALA* 3.1 6.2 + - - +
308A ILE* 2.9 22.1 + - - +
377A ALA* 4.0 13.9 - - + -
380A ASP* 2.9 29.4 + - - -
424A ASP* 2.7 39.2 + - - +
427A PHE* 3.6 44.2 - + + +
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Residues in contact with ALA 305 (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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301A VAL 2.8 18.6 + - - +
302A ILE* 3.7 1.8 - - - +
303A LYS 3.4 2.8 + - - -
304A HIS* 1.3 75.2 - - - +
306A LYS* 1.3 58.5 + - + +
308A ILE* 2.8 10.1 + - - +
309A ASN* 2.8 35.5 + - - +
332A LEU* 3.6 42.4 - - + -
360A PHE* 4.6 12.5 - - + -
410A VAL* 5.1 0.7 - - + -
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Residues in contact with LYS 306 (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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303A LYS 5.2 0.6 + - - -
304A HIS 3.4 0.8 - - - -
305A ALA* 1.3 75.6 - - + +
307A ALA* 1.3 61.8 + - - +
309A ASN* 3.2 23.5 - - - +
332A LEU* 5.5 2.2 - - + -
409A GLN* 3.2 29.8 + - - +
410A VAL 4.0 7.1 + - - -
411A ALA* 3.9 15.7 - - + +
416A GLU* 3.1 31.2 + - + +
417A ALA* 3.5 15.4 - - - -
420A ALA* 3.5 19.1 - - + -
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Residues in contact with ALA 307 (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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304A HIS 3.1 10.2 + - - +
306A LYS* 1.3 75.7 - - - +
308A ILE* 1.3 67.0 + - - +
310A ALA* 3.1 20.4 + - - +
311A LEU* 3.8 9.6 - - - +
420A ALA* 3.6 4.7 - - - +
421A LEU* 3.8 34.5 - - + +
424A ASP* 3.8 19.5 + - + +
427A PHE* 4.0 16.6 - - + -
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Residues in contact with ILE 308 (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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301A VAL* 3.9 21.3 - - + +
304A HIS 2.9 20.0 + - - +
305A ALA* 2.8 8.4 + - - +
307A ALA* 1.3 75.4 - - - +
309A ASN* 1.3 56.7 + - - +
311A LEU* 2.8 26.4 + - - +
312A ALA* 2.8 18.5 + - + +
360A PHE* 4.1 13.5 - - + -
370A CYS 4.9 1.3 - - - +
373A ALA* 4.1 20.9 - - + +
374A LEU* 3.5 37.0 - - + +
377A ALA* 3.6 28.5 - - + -
427A PHE* 4.4 7.0 - - + -
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Residues in contact with ASN 309 (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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305A ALA 2.8 10.5 + - - +
306A LYS* 3.2 17.0 - - - +
308A ILE* 1.3 76.7 - - - +
310A ALA* 1.3 59.0 + - - +
311A LEU 2.9 0.2 - - - -
313A ASN* 2.7 58.5 + - - +
319A TYR* 3.7 18.2 - - - +
322A LEU* 4.7 1.4 - - - +
360A PHE* 3.4 20.8 - - - -
410A VAL* 3.4 14.7 - - - +
411A ALA* 2.7 33.4 + - + +
417A ALA* 3.8 4.5 - - + -
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Residues in contact with ALA 310 (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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307A ALA 3.1 16.1 + - - +
309A ASN* 1.3 77.4 - - - +
311A LEU* 1.3 51.7 + - - +
313A ASN 4.7 1.8 - - - -
314A PRO* 3.7 10.3 - - - +
414A LEU* 5.0 1.8 - - - -
417A ALA* 3.4 33.2 - - - +
418A LEU* 4.1 13.0 - - + +
421A LEU* 3.8 22.0 - - + -
442A TYR* 2.6 30.1 + - - -
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Residues in contact with LEU 311 (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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307A ALA 3.8 15.5 - - - +
308A ILE* 2.8 7.2 + - - +
310A ALA* 1.3 82.1 - - + +
312A ALA* 1.3 58.3 + - - +
313A ASN 3.4 1.6 - - - -
314A PRO* 3.8 5.2 - - - +
365A ALA* 3.2 22.3 - - - +
366A ASN* 4.0 4.5 + - - +
369A LEU* 3.5 32.1 - - + +
370A CYS* 3.7 21.8 - - - +
373A ALA* 3.7 24.0 - - + -
421A LEU* 4.3 18.6 - - + -
428A LEU* 4.9 4.9 - - + -
434A PHE* 4.9 10.5 - - + -
442A TYR* 3.7 27.7 + - + -
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Residues in contact with ALA 312 (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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308A ILE* 2.8 19.4 + - + +
311A LEU* 1.3 73.6 - - - +
313A ASN* 1.3 67.5 + - - +
314A PRO* 3.4 3.4 - - - +
360A PHE* 4.1 5.4 - - + -
361A PRO* 3.4 31.2 - - + -
362A ASP* 3.0 29.1 + - - +
365A ALA* 3.5 7.9 - - - +
370A CYS* 3.5 18.2 - - - -
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Residues in contact with ASN 313 (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* 2.7 40.1 + - - +
312A ALA* 1.3 82.3 - - - +
314A PRO* 1.3 58.6 - - - +
315A THR 3.3 4.4 + - - -
318A SER* 3.6 17.9 - - - -
319A TYR* 2.8 37.3 + - + +
321A ARG* 4.1 0.3 + - - -
322A LEU* 3.3 19.4 - - + +
360A PHE* 2.7 37.1 + - - +
362A ASP* 3.3 10.7 - - - +
414A LEU* 4.0 1.7 - - - +
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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