Contacts of the helix formed by residues 430 - 437 (chain A) in PDB entry 4IQJ
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 SER 430 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A GLU* 2.6 23.7 + - - -
394A ILE* 5.0 0.2 - - - +
403A PHE* 4.8 2.8 - - - -
426A SER 4.4 1.2 + - - -
427A ALA 3.6 3.4 + - - -
428A ALA 3.2 5.6 - - - +
429A GLY* 1.3 74.7 - - - +
431A LEU* 1.3 57.9 + - - +
432A VAL* 3.5 4.0 + - - +
433A ALA* 3.2 25.7 + - - +
434A TYR* 3.0 24.1 + - - +
439A THR* 4.1 0.2 - - - +
443A PRO* 4.3 0.9 - - - -
450A PHE* 3.5 20.9 - - - +
453A PHE* 3.9 19.9 - - - +
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Residues in contact with LEU 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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318A LEU* 4.4 6.5 - - + -
322A TYR* 3.4 34.3 - - + +
383A ILE* 3.9 17.0 - - + +
386A ARG* 3.3 37.7 - - + +
387A ALA* 4.0 13.0 - - + +
390A GLU* 3.0 19.5 + - - +
429A GLY 3.5 3.8 + - - -
430A SER* 1.3 68.7 - - - +
432A VAL* 1.3 56.9 + - - +
434A TYR* 3.2 12.6 + - + +
435A ALA* 2.7 36.7 + - + +
443A PRO* 3.8 14.8 - - + +
444A LEU* 4.0 13.5 - - + -
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Residues in contact with VAL 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 4.4 8.7 - - + -
314A THR* 3.6 23.8 - - + +
387A ALA* 3.9 6.5 - - - +
390A GLU* 2.9 39.3 + - + +
391A LEU* 3.8 29.4 - - + +
394A ILE* 4.1 14.8 - - + -
403A PHE* 5.0 6.1 - - + -
430A SER* 3.8 3.1 - - - +
431A LEU* 1.3 77.3 - - - +
433A ALA* 1.3 58.5 + - - +
435A ALA* 3.6 5.3 - - - +
436A VAL* 3.0 36.4 + - + +
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Residues in contact with ALA 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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403A PHE* 4.9 6.5 - - + -
427A ALA 3.8 13.5 - - - +
430A SER* 3.2 25.6 + - - +
432A VAL* 1.3 80.2 - - - +
434A TYR* 1.3 62.0 + - - +
437A GLY 3.1 3.3 + - - -
438A ILE* 2.8 62.2 + - + -
439A THR* 3.2 4.8 + - + -
453A PHE* 5.6 0.7 - - + -
464A ILE* 5.5 1.8 - - + -
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Residues in contact with TYR 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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321A ARG* 2.8 78.8 + - + +
322A TYR* 3.7 23.3 - + - -
430A SER 3.0 10.6 + - - +
431A LEU* 3.4 12.8 - - + +
433A ALA* 1.3 77.5 - - - +
435A ALA* 1.3 60.3 + - - +
436A VAL 3.4 0.2 + - - -
437A GLY 3.5 3.3 + - - -
439A THR* 3.3 21.7 - - + +
440A ASN* 3.7 1.6 - - - -
441A ILE* 3.0 41.3 - - - -
442A ASP* 3.6 21.0 + - + +
443A PRO* 3.5 17.7 - - + -
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Residues in contact with ALA 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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313A LEU 4.5 0.2 - - - -
314A THR* 3.7 35.4 - - + +
317A GLY* 3.4 22.8 - - - -
318A LEU* 4.6 15.5 - - + +
320A ARG* 5.1 4.0 + - - -
321A ARG* 3.7 15.6 + - - +
431A LEU* 2.7 20.9 + - + +
432A VAL 3.6 4.3 - - - +
434A TYR* 1.3 78.2 - - - +
436A VAL* 1.3 61.3 + - - +
437A GLY 3.5 0.2 + - - -
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Residues in contact with VAL 436 (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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310A LEU* 4.2 15.7 - - + -
313A LEU* 3.9 23.8 - - + -
314A THR* 3.6 34.1 - - - +
320A ARG* 5.5 4.0 + - - -
403A PHE* 6.2 0.7 - - + -
407A GLN* 3.4 40.7 - - + +
411A ASN* 3.9 15.6 + - - +
432A VAL* 3.0 21.6 + - + +
433A ALA* 4.6 2.2 - - - +
435A ALA* 1.3 76.6 - - - +
437A GLY* 1.3 58.0 + - - +
438A ILE* 5.1 3.1 - - + +
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Residues in contact with GLY 437 (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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320A ARG* 6.2 0.9 - - - -
321A ARG* 4.1 14.1 - - - -
407A GLN* 5.0 0.4 - - - -
410A ILE* 3.2 8.5 - - - +
411A ASN* 3.8 7.7 + - - -
414A ARG* 2.7 31.9 + - - -
433A ALA 3.1 4.9 + - - -
434A TYR 3.9 8.1 - - - -
435A ALA 3.4 1.4 - - - -
436A VAL* 1.3 79.2 - - - +
438A ILE* 1.3 62.7 + - - +
439A THR 3.6 2.7 - - - -
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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