Contacts of the helix formed by residues 411 - 421 (chain A) in PDB entry 2IHU
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 GLY 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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410A ILE* 1.3 79.8 - - - +
412A PHE* 1.3 67.3 + - - +
413A PHE* 3.2 5.5 - - - -
414A ARG* 3.1 17.5 + - - +
415A HIS* 3.8 9.4 + - - -
495A LEU* 3.9 7.9 - - - +
600A TP9 3.6 31.6 - - - -
603A TAR 4.6 0.4 + - - -
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Residues in contact with PHE 412 (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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271A TYR* 4.3 6.3 - + - -
275A ILE* 3.8 34.3 - - + -
411A GLY* 1.3 71.7 - - - -
413A PHE* 1.3 62.4 + - - +
414A ARG 3.1 1.2 + - - -
415A HIS* 3.2 15.1 + + - +
416A TYR* 3.5 23.7 - + - -
495A LEU* 3.6 33.5 - - + +
498A LEU* 3.9 17.0 - - + -
561A TYR* 3.4 36.1 - + + -
563A PHE* 3.7 24.2 - + + -
568A PHE* 3.9 20.0 - + - -
600A TP9 2.8 23.5 + - - +
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Residues in contact with PHE 413 (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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384A VAL* 3.9 18.6 - - + +
388A ILE* 4.3 1.4 - - - +
408A SER* 3.2 22.2 - - - -
409A ASP* 3.5 24.2 - - + -
410A ILE 3.3 21.3 - - - -
411A GLY* 4.0 0.7 - - - -
412A PHE* 1.3 78.4 - - - +
414A ARG* 1.3 63.0 - - - +
415A HIS 3.2 0.2 - - - -
416A TYR* 3.1 17.0 + - - +
417A GLY* 3.0 17.8 + - - -
460A ILE* 3.5 31.4 - - + +
461A ALA* 3.5 5.2 - - - -
462A GLY* 3.1 30.5 - - - -
488A VAL* 4.0 10.1 - - + -
561A TYR* 3.6 13.1 + - - +
600A TP9 3.3 21.8 + - - -
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Residues in contact with ARG 414 (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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251A TYR* 3.9 14.2 - - - -
408A SER* 3.5 15.9 - - - +
409A ASP 3.3 25.6 - - - +
410A ILE* 3.6 8.2 - - - +
411A GLY 3.1 18.0 + - - +
413A PHE* 1.3 80.1 - - - +
415A HIS* 1.3 75.8 + - - +
417A GLY* 3.0 4.0 + - - +
418A VAL* 2.9 38.6 + - - +
429A PHE* 4.2 1.4 - - + -
431A THR* 3.0 35.5 + - - +
432A SER 3.0 21.6 + - - -
436A SER* 2.9 23.8 + - - -
603A TAR 2.8 30.7 + - - -
120B HIS* 4.5 0.6 - - - -
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Residues in contact with HIS 415 (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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251A TYR* 3.3 25.6 + + - -
269A THR* 2.7 25.2 + - + +
271A TYR* 3.2 40.8 - + + -
275A ILE* 3.7 22.4 - - + -
411A GLY 3.8 15.7 + - - -
412A PHE* 3.2 9.7 + - + +
413A PHE 3.2 0.4 - - - -
414A ARG* 1.3 93.4 + - - +
416A TYR* 1.3 63.2 + - - +
418A VAL* 3.4 6.5 + - - +
419A LEU* 3.2 28.1 + - - +
495A LEU* 4.8 2.2 - - + -
603A TAR 3.5 19.5 + - - -
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Residues in contact with TYR 416 (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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275A ILE* 3.7 35.4 + - + +
371A PHE* 5.2 2.7 - + - -
384A VAL* 3.6 11.7 - - + -
385A HIS* 3.7 37.1 + - - -
388A ILE* 3.5 15.3 - - + -
412A PHE* 3.5 48.4 - + - -
413A PHE* 3.1 13.8 + - - +
415A HIS* 1.3 75.9 - - - +
417A GLY* 1.3 51.2 + - - +
419A LEU 3.3 0.3 + - - -
420A PHE* 2.8 63.5 + + + +
561A TYR* 4.4 15.1 + + - -
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Residues in contact with GLY 417 (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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254A LYS* 3.9 2.1 + - - -
388A ILE* 3.5 12.9 - - - +
408A SER* 5.3 2.0 - - - -
413A PHE 3.0 12.7 + - - -
414A ARG* 3.0 5.6 + - - -
416A TYR* 1.3 75.5 - - - +
418A VAL* 1.3 59.4 + - - +
421A ALA* 2.8 35.2 + - - +
429A PHE* 3.6 20.6 - - - -
460A ILE* 5.8 3.1 - - - -
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Residues in contact with VAL 418 (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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251A TYR* 3.6 45.3 - - + -
254A LYS* 2.8 28.2 + - - +
267A ALA* 3.8 25.5 + - + +
268A VAL 4.0 7.6 - - - +
269A THR* 4.0 12.8 - - + -
414A ARG* 2.9 28.8 + - - +
415A HIS* 3.6 11.9 - - - +
417A GLY* 1.3 75.4 - - - +
419A LEU* 1.3 56.8 + - - +
429A PHE* 4.0 17.5 - - + -
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Residues in contact with LEU 419 (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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254A LYS* 4.5 3.0 + - - -
267A ALA 4.2 9.9 - - - +
269A THR* 3.8 11.0 - - + -
272A MET* 3.6 50.9 - - + -
275A ILE* 4.0 28.7 - - + -
276A LEU* 4.2 17.5 - - + -
368A ILE* 4.3 21.5 - - + +
415A HIS 3.2 20.2 + - - +
416A TYR 3.3 3.3 + - - +
418A VAL* 1.3 75.3 - - - +
420A PHE* 1.3 75.9 + - + +
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Residues in contact with PHE 420 (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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275A ILE* 4.4 1.6 - - + -
276A LEU* 3.8 20.6 - - + -
368A ILE* 3.8 24.0 - - + -
371A PHE* 3.7 35.7 - + + -
372A LEU* 3.6 36.2 - - + +
385A HIS* 3.9 10.8 - - + -
388A ILE* 3.6 11.7 - - + -
392A ASN* 2.8 29.5 + - - -
416A TYR* 2.8 61.1 + + + +
419A LEU* 1.3 90.6 - - + +
421A ALA* 1.3 56.2 + - - +
422A ARG* 4.7 0.2 - - - -
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Residues in contact with ALA 421 (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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254A LYS* 3.1 22.7 + - - -
388A ILE* 3.6 9.9 - - + +
392A ASN* 3.6 6.1 - - - +
406A ILE* 4.3 14.1 - - + -
417A GLY* 2.8 29.6 + - - +
419A LEU 3.9 0.2 - - - -
420A PHE* 1.3 74.7 - - - +
422A ARG* 1.3 64.8 + - - +
423A ALA 3.5 1.4 + - - -
429A PHE* 3.6 28.0 - - + -
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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