Contacts of the helix formed by residues 421 - 433 (chain A) in PDB entry 5IVK
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 PHE 421 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A SER* 3.5 35.2 - - - -
245A GLY* 4.4 1.8 - - - +
246A ASN* 4.8 1.9 + - - -
249A CYS* 4.8 2.0 - - - -
251A TRP* 4.0 15.0 - + - -
347A ASN* 3.5 19.1 + - - +
351A GLU* 3.6 36.3 - - + -
352A GLY* 5.4 1.3 - - - -
355A PHE* 5.9 5.2 - + - -
416A CYS* 4.3 3.8 - - + -
417A SER 3.3 9.7 + - - +
418A HIS 3.5 2.0 + - - -
420A TYR* 1.3 103.7 - + + +
422A TRP* 1.3 67.9 + - + +
423A PHE 3.4 1.3 - - - -
424A PRO* 3.5 5.1 - - - +
425A MET* 3.1 22.9 + - - +
471A HIS* 3.5 33.9 - + + -
601A DPF 4.4 10.1 - - + -
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Residues in contact with TRP 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASN* 3.6 31.8 - - + +
348A THR 3.7 18.4 + - - -
349A SER 5.8 0.8 - - - -
351A GLU* 4.5 2.4 - - + +
417A SER* 3.0 44.0 + - - +
418A HIS* 3.8 19.7 - - + +
421A PHE* 1.3 76.4 - - + +
423A PHE* 1.3 63.5 + - - +
425A MET* 3.3 40.2 + - + +
426A HIS* 3.0 21.5 + - - +
443A LEU* 6.1 0.4 - - + -
444A TYR 5.0 3.1 - - - -
445A ARG* 4.3 20.6 - - + -
550A VAL* 3.6 27.8 - - + -
552A GLU* 3.6 40.9 + - + +
556A ILE* 4.2 14.2 - - + +
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Residues in contact with PHE 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A PRO* 4.5 6.1 - - + -
418A HIS* 3.0 22.8 + - + +
419A PHE 5.8 0.4 - - - -
422A TRP* 1.3 78.8 - - - +
424A PRO* 1.3 68.0 - - + +
426A HIS* 3.0 11.8 + + + +
427A ARG* 3.0 51.4 + - + +
556A ILE* 4.1 12.3 - - + -
559A TRP* 3.5 49.1 - + + -
560A GLU* 3.5 26.5 - - + -
563A PHE* 3.6 31.6 - + - -
570A PHE* 4.0 12.6 - + - -
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Residues in contact with PRO 424 (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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246A ASN* 3.8 3.9 + - - +
248A ILE* 3.6 17.8 - - + +
249A CYS* 3.6 40.8 - - - +
250A PRO* 4.0 3.4 - - + -
418A HIS 3.4 10.1 - - - +
419A PHE 3.6 16.8 - - - +
420A TYR 3.8 12.8 - - - +
421A PHE 3.5 8.7 - - - +
423A PHE* 1.3 96.7 - - + +
425A MET* 1.3 60.6 + - - +
427A ARG* 3.5 3.7 + - - -
428A LEU* 3.0 23.2 + - - +
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Residues in contact with MET 425 (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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246A ASN* 3.8 12.0 - - - +
345A MET* 4.4 33.2 - - + -
346A GLY* 4.8 6.7 - - - -
347A ASN* 3.6 17.7 - - - +
421A PHE 3.1 17.9 + - - +
422A TRP* 3.5 38.4 - - + +
423A PHE 3.1 0.2 - - - -
424A PRO* 1.3 75.5 - - - +
426A HIS* 1.3 58.8 + - - +
428A LEU* 3.3 3.9 + - - +
429A LEU* 2.8 52.4 + - + +
443A LEU* 4.7 18.8 - - + -
536A TYR* 5.0 7.6 - - + -
550A VAL* 5.9 0.2 - - + -
556A ILE* 5.3 2.0 - - + -
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Residues in contact with HIS 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A TRP 3.0 9.3 + - - +
423A PHE* 3.0 12.6 + + - +
425A MET* 1.3 77.0 - - - +
427A ARG* 1.3 61.9 + - - +
429A LEU* 3.2 2.2 + - - +
430A GLN* 3.0 40.1 + - + +
536A TYR* 2.5 46.5 + + + -
553A MET* 4.8 8.3 - - + -
556A ILE* 3.2 39.5 - - + +
557A LYS* 4.8 4.2 - - + +
560A GLU* 2.7 29.7 + - - -
570A PHE* 3.6 21.4 - + - -
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Residues in contact with ARG 427 (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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248A ILE* 4.2 22.3 + - + +
330A ARG* 3.8 17.1 - - - +
377A PRO* 4.5 5.5 - - - +
379A GLU* 2.7 33.1 + - - +
423A PHE* 3.0 41.3 + - + +
424A PRO* 3.8 7.9 - - - +
426A HIS* 1.3 75.9 - - - +
428A LEU* 1.3 63.0 + - - +
430A GLN* 3.4 1.6 + - - +
431A LEU* 3.0 26.8 + - - +
563A PHE* 3.6 16.0 - - - -
569A LEU 2.8 25.1 + - - -
570A PHE* 2.8 48.6 + - + +
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Residues in contact with LEU 428 (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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225A HIS* 3.5 39.7 - - + +
242A LEU* 4.1 1.3 - - + -
246A ASN* 3.9 20.0 - - + +
248A ILE* 4.8 7.4 - - + +
333A VAL* 4.1 22.9 - - + -
339A ASN* 5.6 0.9 - - - +
345A MET* 3.5 38.4 - - + -
424A PRO 3.0 18.3 + - - +
425A MET 3.6 3.6 - - - +
426A HIS 3.2 0.2 - - - -
427A ARG* 1.3 74.9 - - - +
429A LEU* 1.3 68.0 + - - +
431A LEU* 3.3 4.1 + - - -
432A ARG* 2.8 34.2 + - + +
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Residues in contact with LEU 429 (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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345A MET* 4.5 17.5 - - + -
425A MET* 2.8 35.9 + - + +
426A HIS 3.2 0.4 + - - +
428A LEU* 1.3 73.8 - - - +
430A GLN* 1.3 62.5 + - - +
432A ARG* 3.3 7.0 + - - +
433A PHE* 3.1 39.1 + - + -
441A VAL* 4.2 33.4 - - + -
443A LEU* 4.2 20.0 - - + -
529A ILE* 5.3 2.2 - - + -
536A TYR* 3.3 51.4 - - + +
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Residues in contact with GLN 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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426A HIS* 3.0 38.3 + - + +
427A ARG 4.0 0.7 - - - +
429A LEU* 1.3 75.5 - - - +
431A LEU* 1.3 63.0 + - - +
433A PHE* 3.4 29.5 + - - +
434A ASN* 3.6 17.5 + - - +
530A GLU 5.6 0.2 + - - -
531A LYS 4.7 8.4 + - - +
533A ASP 5.1 5.7 + - - -
536A TYR* 2.9 32.7 + - - -
560A GLU* 5.7 0.4 - - - +
570A PHE* 3.8 22.7 - - + -
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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
----------------------------------------------------------
248A ILE* 4.8 2.9 - - + -
330A ARG* 3.5 59.0 - - + +
333A VAL* 3.6 25.1 - - + -
334A LYS* 3.0 34.3 - - + +
427A ARG 3.0 18.9 + - - +
428A LEU* 3.8 3.6 - - - +
430A GLN* 1.3 77.2 - - - +
432A ARG* 1.3 61.0 + - - +
434A ASN* 3.2 14.3 + - + +
435A HIS* 3.5 18.3 + - - +
570A PHE 4.8 6.1 - - - +
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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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333A VAL* 4.1 14.1 - - + +
339A ASN* 3.1 50.0 + - + +
341A ILE 4.5 3.6 + - - -
343A THR* 4.6 7.9 + - - -
345A MET* 4.9 17.0 - - - -
428A LEU* 2.8 24.0 + - + +
429A LEU* 3.7 7.2 - - - +
431A LEU* 1.3 73.5 - - - +
433A PHE* 1.3 78.4 + - - +
434A ASN 2.8 12.0 + - - -
435A HIS 3.0 11.8 + - - -
436A THR* 3.3 20.7 + - - +
439A THR* 2.8 34.4 + - - -
440A PRO 4.2 6.1 + - - -
441A VAL* 3.6 28.8 - - - +
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Residues in contact with PHE 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 LEU* 3.1 32.4 + - + -
430A GLN* 3.8 31.9 - - - +
431A LEU 3.3 1.0 - - - -
432A ARG* 1.3 98.4 - - - +
434A ASN* 1.3 69.9 + - - +
435A HIS 3.6 0.2 - - - -
436A THR* 3.9 14.9 - - + +
441A VAL* 4.1 8.7 - - + -
529A ILE* 3.6 47.6 - - + -
530A GLU 3.9 13.2 - - - -
531A LYS* 4.3 38.9 + - + +
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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