Contacts of the helix formed by residues 425 - 430 (chain D) 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 ARG 425 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421D LEU 3.3 13.4 + - - +
422D ASP* 2.7 47.7 + - - +
423D LEU 2.9 8.1 + - - +
424D ASP* 1.3 75.5 - - - +
426D GLU* 1.3 79.6 + - - +
427D PHE 3.3 0.4 - - - -
428D LEU* 3.1 21.6 + - - +
429D LYS* 3.3 19.6 + - + +
436D ASP* 3.1 37.7 + - - +
439D ILE* 4.0 26.4 - - + +
440D ASP* 2.9 37.2 + - - -
443D ILE* 4.4 2.2 - - - +
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Residues in contact with GLU 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423D LEU 5.4 3.6 - - - +
424D ASP* 3.5 2.8 + - - +
425D ARG* 1.3 85.9 - - + +
427D PHE* 1.3 63.6 + - - +
429D LYS* 3.0 51.3 + - - +
430D ALA* 3.3 10.2 + - - +
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Residues in contact with PHE 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304D HIS* 3.6 47.8 - + + +
307D ALA* 4.0 11.9 - - + -
308D ILE* 4.4 7.9 - - + -
373D ALA* 3.7 4.0 - - + -
376D MET* 3.5 26.9 - - - +
377D ALA* 3.5 44.2 - - + -
380D ASP* 4.0 19.6 - - + +
424D ASP* 3.0 33.1 + - - -
426D GLU* 1.3 77.0 - - - +
428D LEU* 1.3 95.9 + - + +
430D ALA* 3.6 9.6 - - - +
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D LEU* 4.9 5.2 - - + -
373D ALA* 3.9 24.0 - - + -
376D MET* 3.7 10.5 - - + +
421D LEU* 3.5 32.3 - - + -
425D ARG* 3.1 11.4 + - - +
426D GLU 3.0 0.4 - - - -
427D PHE* 1.3 124.2 - - + +
429D LYS* 1.3 59.4 - - - +
430D ALA 3.1 6.3 + - - -
433D VAL* 3.6 7.6 - - - +
434D PHE* 3.1 55.7 + - + +
439D ILE* 4.2 5.8 - - + -
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Residues in contact with LYS 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425D ARG* 3.3 21.6 - - - +
426D GLU* 3.0 42.0 + - - +
428D LEU* 1.3 75.1 - - - +
430D ALA* 1.3 65.9 + - - +
431D GLY 3.4 0.3 + - - -
432D GLY* 2.9 19.2 + - - -
433D VAL 4.4 0.2 - - - -
434D PHE 3.2 20.4 - - - +
435D THR* 4.7 0.4 - - - -
436D ASP* 2.8 48.8 + - - +
439D ILE* 4.4 7.2 - - + -
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Residues in contact with ALA 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.7 21.5 - - + +
376D MET* 3.2 8.4 - - + +
383D LYS* 4.8 7.6 - - - +
426D GLU 3.3 7.6 + - - +
427D PHE* 3.6 19.1 - - - +
428D LEU 3.1 0.8 - - - -
429D LYS* 1.3 77.6 - - - +
431D GLY* 1.3 64.2 + - - +
432D GLY 3.0 1.2 + - - -
433D VAL* 3.2 19.8 - - - +
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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