Contacts of the helix formed by residues 425 - 430 (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 ARG 425 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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421E LEU 3.3 12.7 + - - +
422E ASP* 2.7 47.6 + - - +
423E LEU 2.9 8.5 + - - +
424E ASP* 1.3 76.4 - - - +
426E GLU* 1.3 80.0 + - - +
427E PHE 3.3 0.4 - - - -
428E LEU* 3.1 21.2 + - - +
429E LYS* 3.3 21.7 + - + +
436E ASP* 3.1 38.3 + - - +
439E ILE* 4.0 26.7 - - + +
440E ASP* 2.9 36.8 + - - -
443E ILE* 4.4 1.8 - - - +
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Residues in contact with GLU 426 (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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423E LEU 4.7 3.6 + - - +
424E ASP* 3.5 2.6 + - - +
425E ARG* 1.3 85.8 - - + +
427E PHE* 1.3 63.0 + - - +
429E LYS* 3.0 50.6 + - - +
430E ALA* 3.3 10.0 + - - +
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Residues in contact with PHE 427 (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* 3.6 48.2 - + + +
307E ALA* 4.0 11.2 - - + -
308E ILE* 4.4 7.6 - - + -
373E ALA* 3.7 4.0 - - + -
376E MET* 3.5 26.6 - - - +
377E ALA* 3.5 43.7 - - + -
380E ASP* 4.0 20.1 - - + +
424E ASP* 3.0 32.9 + - - -
426E GLU* 1.3 76.3 - - - +
428E LEU* 1.3 96.7 + - + +
430E ALA* 3.6 9.5 - - - +
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Residues in contact with LEU 428 (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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311E LEU* 4.9 4.9 - - + -
373E ALA* 3.9 23.6 - - + -
376E MET* 3.7 10.3 - - + +
421E LEU* 3.5 32.1 - - + -
425E ARG* 3.1 11.8 + - - +
426E GLU 3.0 0.2 - - - -
427E PHE* 1.3 123.3 - - + +
429E LYS* 1.3 60.2 - - - +
430E ALA 3.1 6.0 + - - -
433E VAL* 3.6 7.4 - - - +
434E PHE* 3.1 56.0 + - + +
439E ILE* 4.2 6.3 - - + -
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Residues in contact with LYS 429 (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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425E ARG* 3.3 22.1 - - - +
426E GLU* 3.0 41.7 + - - +
428E LEU* 1.3 74.2 - - - +
430E ALA* 1.3 65.5 + - - +
431E GLY 3.4 0.3 + - - -
432E GLY* 2.9 19.3 + - - -
434E PHE 3.2 20.8 - - - +
435E THR* 4.7 0.7 - - - -
436E ASP* 2.8 47.6 + - - +
439E ILE* 4.4 7.4 - - + -
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Residues in contact with ALA 430 (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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114E TYR* 3.7 22.2 - - + +
376E MET* 3.2 21.2 - - + +
383E LYS* 4.8 7.4 - - - +
426E GLU 3.3 6.8 + - - +
427E PHE* 3.6 20.0 - - - +
428E LEU 3.1 1.0 - - - -
429E LYS* 1.3 77.3 - - - +
431E GLY* 1.3 63.2 + - - +
432E GLY 3.0 1.2 + - - -
433E VAL* 3.2 6.9 - - - +
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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