Contacts of the helix formed by residues 304 - 313 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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300I GLY* 3.0 24.4 + - - +
301I VAL 3.6 2.2 - - - -
303I LYS* 1.3 101.3 - - + +
305I ALA* 1.3 64.1 + - - +
306I LYS 3.4 2.2 - - - -
307I ALA* 3.1 6.3 + - - +
308I ILE* 2.9 21.6 + - - +
377I ALA* 4.0 12.6 - - + -
380I ASP* 2.9 29.6 + - - -
424I ASP* 2.7 40.7 + - - +
427I PHE* 3.6 42.5 - + + +
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Residues in contact with ALA 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301I VAL 2.8 18.0 + - - +
302I ILE* 3.7 1.8 - - - +
303I LYS 3.4 2.8 + - - -
304I HIS* 1.3 74.9 - - - +
306I LYS* 1.3 59.1 + - + +
308I ILE* 2.8 10.9 + - - +
309I ASN* 2.8 35.0 + - - +
332I LEU* 3.6 42.6 - - + -
360I PHE* 4.6 10.7 - - + -
410I VAL* 5.1 0.9 - - + -
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Residues in contact with LYS 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I LYS 5.2 0.8 + - - -
304I HIS 3.4 0.4 - - - -
305I ALA* 1.3 77.5 - - + +
307I ALA* 1.3 61.9 + - - +
309I ASN* 3.2 23.1 + - - +
332I LEU* 5.5 2.9 - - + -
409I GLN* 3.2 29.6 + - - +
410I VAL 4.0 6.9 + - - -
411I ALA* 3.9 15.7 - - + +
416I GLU* 3.1 30.9 + - + +
417I ALA* 3.5 16.3 - - - +
420I ALA* 3.5 17.3 - - + -
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Residues in contact with ALA 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304I HIS 3.1 9.8 + - - +
306I LYS* 1.3 74.8 - - - +
308I ILE* 1.3 66.4 + - - +
310I ALA* 3.1 20.4 + - - +
311I LEU* 3.8 9.3 - - - +
420I ALA* 3.6 5.5 - - - +
421I LEU* 3.8 34.3 - - + +
424I ASP* 3.8 19.0 + - + +
427I PHE* 4.0 16.6 - - + -
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Residues in contact with ILE 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301I VAL* 3.9 22.0 - - + +
304I HIS 2.9 18.2 + - - +
305I ALA* 2.8 8.6 + - - +
307I ALA* 1.3 76.0 - - - +
309I ASN* 1.3 57.9 + - - +
311I LEU* 2.8 26.6 + - - +
312I ALA* 2.8 19.4 + - + +
360I PHE* 4.1 12.8 - - + -
370I CYS 4.9 0.9 - - - +
373I ALA* 4.1 20.9 - - + +
374I LEU* 3.5 36.3 - - + +
377I ALA* 3.6 27.8 - - + -
427I PHE* 4.4 6.7 - - + -
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Residues in contact with ASN 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305I ALA 2.8 11.0 + - - +
306I LYS* 3.2 17.7 - - - +
308I ILE* 1.3 77.1 - - - +
310I ALA* 1.3 57.8 + - - +
311I LEU 2.9 0.2 - - - -
313I ASN* 2.7 58.2 + - - +
319I TYR* 3.7 17.0 - - - +
322I LEU* 4.7 1.2 - - - +
360I PHE* 3.4 21.2 - - - -
410I VAL* 3.4 14.2 - - - +
411I ALA* 2.7 33.8 + - + +
417I ALA* 3.8 4.3 - - + -
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Residues in contact with ALA 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307I ALA 3.1 15.6 + - - +
309I ASN* 1.3 77.9 - - - +
311I LEU* 1.3 49.9 + - - +
313I ASN 4.7 1.8 - - - -
314I PRO* 3.7 9.3 - - - +
414I LEU* 5.0 1.6 - - - -
417I ALA* 3.4 33.1 - - - +
418I LEU* 4.1 12.6 - - + +
421I LEU* 3.8 23.6 - - + -
442I TYR* 2.6 30.9 + - + -
446I ARG* 5.3 0.2 - - - +
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Residues in contact with LEU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307I ALA 3.8 16.2 - - - +
308I ILE* 2.8 7.2 + - - +
310I ALA* 1.3 80.5 - - + +
312I ALA* 1.3 58.8 + - - +
313I ASN 3.4 1.1 - - - -
314I PRO* 3.8 4.4 - - - +
365I ALA* 3.2 22.9 - - - +
366I ASN* 4.0 4.2 + - - +
369I LEU* 3.5 31.6 - - + +
370I CYS* 3.7 21.1 - - - +
373I ALA* 3.7 23.6 - - + -
421I LEU* 4.3 17.9 - - + -
428I LEU* 4.9 4.7 - - + -
434I PHE* 4.9 11.2 - - + -
442I TYR* 3.7 28.1 + - + -
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Residues in contact with ALA 312 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308I ILE* 2.8 19.0 + - + +
311I LEU* 1.3 73.6 - - - +
313I ASN* 1.3 68.1 + - - +
314I PRO* 3.4 3.4 - - - +
360I PHE* 4.1 5.4 - - + -
361I PRO* 3.4 31.0 - - + -
362I ASP* 3.0 28.4 + - - +
365I ALA* 3.5 8.7 - - - +
370I CYS* 3.5 19.1 - - - -
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Residues in contact with ASN 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309I ASN* 2.7 40.8 + - - +
312I ALA* 1.3 81.6 - - - +
314I PRO* 1.3 57.7 - - - +
315I THR 3.3 4.7 + - - -
318I SER* 3.6 17.0 - - - -
319I TYR* 2.8 38.8 + - + +
321I ARG* 4.1 0.3 + - - -
322I LEU* 3.3 19.1 - - + +
360I PHE* 2.7 36.7 + - - +
362I ASP* 3.3 11.6 - - - +
414I LEU* 4.0 1.4 - - - +
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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