Contacts of the helix formed by residues 428 - 435 (chain A) in PDB entry 4FE1
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 ASN 428 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339A ALA* 4.4 3.4 - - + -
340A GLY 3.2 15.3 - - - +
342A LYS* 3.1 31.0 + - + +
344A LEU* 3.9 13.9 - - - +
424A MET 4.3 0.2 + - - -
425A ASN* 3.0 39.0 + - - +
426A GLN 3.1 4.6 + - - +
427A ASN* 1.3 83.2 - - - +
429A VAL* 1.3 66.6 + - + +
430A LEU* 3.5 4.7 - - - +
431A ASP* 2.9 24.6 + - - +
432A ARG* 3.1 20.2 + - - +
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Residues in contact with VAL 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A THR* 3.7 34.1 - - + -
340A GLY* 2.8 29.1 + - - +
341A HIS* 3.7 27.4 - - + +
344A LEU* 3.8 14.6 - - + -
428A ASN* 1.3 71.2 - - - +
430A LEU* 1.3 60.8 + - - +
432A ARG* 3.4 7.5 + - - +
433A VAL* 2.8 36.5 + - + +
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Residues in contact with LEU 430 (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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344A LEU* 4.5 15.3 - - + -
347A VAL* 5.0 1.8 - - + -
415A PHE* 4.1 25.4 - - + -
416A MET* 4.2 13.2 - - - -
420A TYR* 4.5 3.8 - - + -
425A ASN* 3.5 28.3 - - + +
428A ASN* 3.2 13.1 + - - +
429A VAL* 1.3 78.2 - - - +
431A ASP* 1.3 65.5 + - - +
433A VAL* 3.1 13.7 + - + +
434A LEU* 3.0 46.4 + - + +
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Residues in contact with ASP 431 (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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420A TYR* 4.5 9.3 + - - +
425A ASN* 3.2 28.0 + - + +
426A GLN* 4.9 0.7 - - - -
427A ASN* 3.3 25.2 + - - +
428A ASN* 2.9 10.8 + - - +
430A LEU* 1.3 76.2 - - - +
432A ARG* 1.3 57.4 + - - +
434A LEU* 3.3 12.8 + - - +
435A ARG* 3.0 57.7 + - - +
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Residues in contact with ARG 432 (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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335A PRO 4.4 4.8 + - - -
336A PHE* 2.6 36.1 + - - +
337A THR* 3.4 13.8 - - + +
338A GLY* 3.2 10.4 - - - +
427A ASN* 2.3 59.2 + - - +
428A ASN 3.1 18.4 + - - +
429A VAL* 3.8 5.8 - - - +
430A LEU 3.2 0.2 - - - -
431A ASP* 1.3 76.9 - - - +
433A VAL* 1.3 62.8 + - - +
435A ARG* 3.3 28.6 + - - +
436A HIS* 2.8 21.6 + - + -
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Residues in contact with VAL 433 (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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429A VAL* 2.8 30.7 + - + +
430A LEU* 3.1 14.8 + - + +
432A ARG* 1.3 73.7 - - - +
434A LEU* 1.3 74.0 + - + +
436A HIS* 3.2 28.6 + - + -
437A ARG* 3.3 13.5 + - - +
440A ILE* 4.4 9.2 - - + +
558A LEU* 3.5 28.7 - - + +
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Residues in contact with LEU 434 (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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416A MET* 3.7 37.0 - - + -
420A TYR* 3.9 26.0 - - + +
430A LEU* 3.0 27.9 + - + +
431A ASP* 3.3 11.6 + - - +
433A VAL* 1.3 79.7 - - + +
435A ARG* 1.3 63.2 + - + +
436A HIS 3.4 1.0 + - - -
437A ARG* 3.4 32.4 + - - +
558A LEU* 3.8 35.4 - - + +
561A ARG* 5.6 0.9 - - - -
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Residues in contact with ARG 435 (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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427A ASN* 3.1 27.1 + - - -
431A ASP* 3.0 41.1 + - - +
432A ARG* 3.3 23.0 + - - +
433A VAL 3.1 0.8 - - - -
434A LEU* 1.3 80.3 - - + +
436A HIS* 1.3 58.2 + - - +
437A ARG* 3.6 0.7 - - - -
438A ASP* 5.8 0.2 - - - +
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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