Contacts of the helix formed by residues 304 - 313 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300E GLY* 3.0 24.3 + - - +
301E VAL 3.6 1.6 - - - -
303E LYS* 1.3 100.9 - - + +
305E ALA* 1.3 64.7 + - - +
306E LYS 3.4 2.2 - - - -
307E ALA* 3.1 5.4 + - - +
308E ILE* 2.9 21.5 + - - +
377E ALA* 4.0 13.7 - - + -
380E ASP* 2.9 30.2 + - - -
424E ASP* 2.7 40.0 + - - +
427E PHE* 3.6 43.1 - + + +
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Residues in contact with ALA 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E VAL 2.8 18.0 + - - +
302E ILE 3.7 1.8 - - - +
303E LYS 3.4 2.6 + - - -
304E HIS* 1.3 74.9 - - - +
306E LYS* 1.3 59.1 + - - +
308E ILE* 2.8 11.1 + - - +
309E ASN* 2.8 35.2 + - - +
332E LEU* 3.6 42.4 - - + -
360E PHE* 4.6 12.3 - - + -
410E VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303E LYS 5.2 0.6 + - - -
304E HIS 3.4 0.8 - - - -
305E ALA* 1.3 76.0 - - + +
307E ALA* 1.3 61.3 + - - +
309E ASN* 3.2 23.3 + - - +
332E LEU* 5.5 2.7 - - + -
409E GLN* 3.2 29.2 + - - +
410E VAL 4.0 7.3 + - - -
411E ALA* 3.9 16.2 - - + +
416E GLU* 3.1 32.0 + - + +
417E ALA* 3.5 16.3 - - - -
420E ALA* 3.5 18.6 - - + -
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Residues in contact with ALA 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304E HIS 3.1 9.6 + - - +
306E LYS* 1.3 75.8 - - - +
308E ILE* 1.3 66.1 + - - +
310E ALA* 3.1 20.3 + - - +
311E LEU* 3.8 9.8 - - - +
420E ALA* 3.6 5.4 - - - +
421E LEU* 3.8 34.8 - - + +
424E ASP* 3.8 18.4 + - + +
427E PHE* 4.0 17.3 - - + -
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Residues in contact with ILE 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301E VAL* 3.9 21.1 - - + +
304E HIS 2.9 19.3 + - - +
305E ALA* 2.8 8.8 + - - +
307E ALA* 1.3 76.7 - - - +
309E ASN* 1.3 56.6 + - - +
311E LEU* 2.8 26.8 + - + +
312E ALA* 2.8 18.7 + - + +
360E PHE* 4.1 12.8 - - + -
370E CYS 4.9 0.9 - - - +
373E ALA* 4.1 20.0 - - + +
374E LEU* 3.5 37.2 - - + +
377E ALA* 3.6 28.3 - - + -
427E PHE* 4.4 7.0 - - + -
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Residues in contact with ASN 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305E ALA 2.8 10.5 + - - +
306E LYS* 3.2 17.5 - - - +
307E ALA 3.1 0.2 - - - -
308E ILE* 1.3 76.9 - - - +
310E ALA* 1.3 58.8 + - - +
313E ASN* 2.7 58.8 + - - +
319E TYR* 3.7 16.4 - - - +
322E LEU* 4.7 1.4 - - - +
360E PHE* 3.4 21.2 - - - -
410E VAL* 3.4 14.6 - - - +
411E ALA* 2.7 33.4 + - + +
417E ALA* 3.8 4.5 - - + -
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Residues in contact with ALA 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E ALA 3.1 15.0 + - - +
309E ASN* 1.3 77.6 - - - +
311E LEU* 1.3 52.6 + - + +
313E ASN 4.7 1.8 - - - -
314E PRO* 3.7 9.3 - - - +
414E LEU* 5.0 1.6 - - - -
417E ALA* 3.4 33.8 - - - +
418E LEU* 4.1 12.1 - - + +
421E LEU* 3.8 23.1 - - + -
442E TYR* 2.6 30.1 + - - -
446E ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307E ALA 3.8 15.5 - - - +
308E ILE* 2.8 7.2 + - - +
310E ALA* 1.3 82.9 - - + +
312E ALA* 1.3 59.0 + - - +
313E ASN 3.4 1.6 - - - -
314E PRO* 3.8 4.8 - - - +
365E ALA* 3.2 22.7 - - - +
366E ASN* 4.0 4.0 + - - +
369E LEU* 3.5 32.1 - - + +
370E CYS* 3.7 21.6 - - - +
373E ALA* 3.7 24.5 - - + -
421E LEU* 4.3 19.1 - - + -
428E LEU* 4.9 4.7 - - + -
434E PHE* 4.9 10.5 - - + -
442E TYR* 3.7 28.0 + - + -
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Residues in contact with ALA 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308E ILE* 2.8 18.9 + - + +
311E LEU* 1.3 73.4 - - - +
313E ASN* 1.3 68.2 + - - +
314E PRO* 3.4 3.6 - - - +
360E PHE* 4.1 5.2 - - + -
361E PRO* 3.4 31.0 - - + -
362E ASP* 3.0 28.6 + - - +
365E ALA* 3.5 8.8 - - - +
370E CYS* 3.5 18.8 - - - -
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Residues in contact with ASN 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309E ASN* 2.7 41.1 + - - +
312E ALA* 1.3 82.3 - - - +
314E PRO* 1.3 59.4 - - - +
315E THR 3.3 4.0 + - - -
318E SER* 3.6 17.9 - - - -
319E TYR* 2.8 37.7 + - + +
321E ARG* 4.1 0.7 + - - -
322E LEU* 3.3 18.6 - - + +
360E PHE* 2.7 36.6 + - - +
362E ASP* 3.3 10.4 - - - +
414E 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