Contacts of the helix formed by residues 399 - 415 (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 PHE 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A TYR* 5.3 10.8 - + + -
295A ILE* 4.4 15.0 - - + -
394A ILE* 2.9 12.1 + - + +
397A MET* 3.5 46.2 - - + -
398A GLY* 1.3 86.9 - - - +
400A PRO* 1.3 69.1 - - - +
401A GLY 3.2 2.7 - - - +
402A TYR* 3.0 29.3 + - + +
403A PHE* 3.2 20.7 - - + -
454A LEU* 4.3 11.4 - - + -
459A VAL* 4.5 10.3 - - + -
460A SER 3.6 32.5 - - - -
461A MET* 4.0 16.4 - - + -
462A PRO* 4.1 16.6 - - + -
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Residues in contact with PRO 400 (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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306A GLU* 3.9 17.3 - - + +
307A ALA* 3.7 39.0 - - + +
310A LEU* 3.8 22.1 - - + +
394A ILE* 3.9 8.4 - - + +
395A GLU* 4.7 6.3 - - + +
398A GLY* 3.1 12.6 - - - +
399A PHE* 1.3 92.8 - - - +
401A GLY* 1.3 64.7 + - - +
402A TYR 3.3 0.3 + - - -
403A PHE* 3.5 4.0 + - - +
404A LEU* 3.3 26.8 + - - +
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Residues in contact with GLY 401 (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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295A ILE* 5.1 8.1 - - - -
296A PRO 5.6 0.4 - - - -
298A PHE* 4.8 1.5 - - - +
306A GLU* 3.5 30.5 + - - -
399A PHE* 3.2 0.8 - - - +
400A PRO* 1.3 83.8 - - - +
402A TYR* 1.3 57.1 + - - +
404A LEU* 3.5 6.0 + - - +
405A ILE* 3.0 41.0 + - - +
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Residues in contact with TYR 402 (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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295A ILE* 4.8 10.1 - - + +
399A PHE* 3.0 23.3 + - + +
401A GLY* 1.3 78.6 - - - +
403A PHE* 1.3 69.0 + + - +
405A ILE* 3.5 4.9 + - - +
406A VAL* 3.0 36.4 + - + +
461A MET* 4.9 15.7 - - + +
462A PRO* 2.8 43.3 + - + -
463A ASP* 3.8 1.2 - - - -
464A ILE* 3.0 44.2 + - + +
615A LEU* 3.6 29.4 - - + -
616A LYS 4.7 0.6 + - - -
617A MET* 3.1 31.8 - - + +
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Residues in contact with PHE 403 (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* 3.9 22.2 - - + -
394A ILE* 3.5 47.8 - - + -
399A PHE* 3.2 31.4 - - + -
400A PRO 4.0 1.1 - - - +
401A GLY 3.4 0.4 - - - -
402A TYR* 1.3 80.5 - + - +
404A LEU* 1.3 62.8 + - - +
406A VAL* 3.0 6.6 + - - +
407A GLN* 2.8 35.2 + - + +
430A SER* 4.8 7.6 - - - -
432A VAL* 5.0 6.1 - - + -
433A ALA* 4.9 5.4 - - + -
436A VAL* 6.2 1.1 - - + -
438A ILE* 3.7 22.8 - - + +
450A PHE* 5.5 0.2 - + - -
453A PHE* 3.8 31.9 - + - -
454A LEU* 4.1 6.5 - - + -
462A PRO* 5.0 0.9 - - + -
464A ILE* 4.1 11.4 - - + -
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Residues in contact with LEU 404 (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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298A PHE* 3.6 29.1 - - + -
306A GLU* 3.4 40.8 - - + +
309A TYR* 3.4 32.5 - - + -
310A LEU* 4.1 16.8 - - + +
313A LEU* 3.6 20.4 - - + -
400A PRO 3.3 13.5 + - - +
401A GLY* 3.7 6.7 - - - +
403A PHE* 1.3 76.7 - - - +
405A ILE* 1.3 61.0 + - - +
407A GLN* 3.7 8.7 + - + +
408A ASP* 3.3 22.7 + - - +
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Residues in contact with ILE 405 (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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295A ILE* 5.1 0.4 - - + -
296A PRO* 3.5 47.8 - - + +
297A ARG 4.4 2.9 - - - +
298A PHE* 3.9 15.7 - - + -
401A GLY 3.0 22.7 + - - +
402A TYR* 3.8 4.5 - - - +
403A PHE 3.2 0.2 - - - -
404A LEU* 1.3 75.3 - - - +
406A VAL* 1.3 63.9 + - + +
408A ASP* 3.6 9.2 - - - +
409A TYR* 3.2 20.1 - - + -
484A TYR* 3.2 38.7 + - + +
581A ILE* 4.3 17.0 - - + -
615A LEU* 4.4 12.1 - - + -
617A MET* 5.7 0.4 - - - -
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Residues in contact with VAL 406 (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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402A TYR* 3.0 42.8 - - + +
403A PHE* 3.0 5.4 + - - +
405A ILE* 1.3 79.0 - - + +
407A GLN* 1.3 64.8 + - - +
408A ASP 3.4 0.7 + - - -
409A TYR* 3.6 17.5 - - - +
410A ILE* 3.2 35.7 + - + +
438A ILE* 3.9 13.9 - - + -
464A ILE* 3.8 25.8 - - + -
466A THR* 4.9 0.4 - - - +
617A MET* 3.9 23.8 - - + -
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Residues in contact with GLN 407 (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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298A PHE* 5.1 3.6 - - - -
309A TYR* 4.9 4.6 + - - -
310A LEU* 6.0 0.2 - - + -
313A LEU* 3.4 25.1 - - + +
403A PHE 2.8 20.2 + - - +
404A LEU* 3.7 19.1 + - - +
406A VAL* 1.3 76.6 - - - +
408A ASP* 1.3 71.4 + - - +
410A ILE* 4.2 4.7 - - - -
411A ASN* 2.9 52.7 + - - +
436A VAL* 3.4 34.7 - - + +
438A ILE* 3.8 18.6 - - + +
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Residues in contact with ASP 408 (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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298A PHE* 3.8 18.2 - - + -
404A LEU 3.3 16.3 + - - +
405A ILE 3.6 8.1 - - - +
406A VAL 3.2 0.6 - - - -
407A GLN* 1.3 89.4 + - - +
409A TYR* 1.3 57.7 + - - +
411A ASN* 3.7 3.8 - - - +
412A TRP* 2.9 25.5 + - - +
479A TYR* 2.6 34.0 + - - -
483A ARG* 3.4 18.9 + - - -
484A TYR* 3.8 7.6 + - - -
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Residues in contact with TYR 409 (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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405A ILE* 3.2 34.3 - - + -
406A VAL* 3.6 21.4 - - + +
408A ASP* 1.3 77.2 - - - +
410A ILE* 1.3 74.1 + - + +
412A TRP* 3.4 9.1 - - - +
413A ALA* 2.9 27.9 + - - +
464A ILE 5.0 0.5 + - - -
466A THR* 4.6 6.5 + - - -
468A PHE* 4.2 4.3 - + - -
476A VAL* 4.0 20.9 - - + +
479A TYR* 3.7 23.8 - - + -
480A VAL* 4.0 18.8 - - + -
484A TYR* 5.2 4.3 - + - -
581A ILE* 4.8 2.2 - - + -
617A MET* 2.8 36.3 - - + -
619A PHE* 3.2 32.0 - + - -
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Residues in contact with ILE 410 (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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406A VAL* 3.2 25.1 - - + +
407A GLN 3.4 4.4 + - - +
408A ASP 3.2 0.6 - - - -
409A TYR* 1.3 89.1 - - + +
411A ASN* 1.3 58.8 + - - +
413A ALA* 3.0 21.5 + - - +
414A ARG* 3.1 31.1 + - - +
420A VAL* 3.9 11.6 - - + +
437A GLY 3.2 22.4 - - - +
438A ILE* 3.6 39.5 - - + +
466A THR* 4.1 23.8 - - + +
468A PHE* 4.4 2.5 - - + -
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Residues in contact with ASN 411 (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* 5.9 0.5 + - - -
407A GLN* 2.9 46.5 + - - +
408A ASP* 3.7 4.3 - - - +
410A ILE* 1.3 71.3 - - - +
412A TRP* 1.3 64.6 + - - +
414A ARG* 3.5 13.3 + - - +
415A GLY* 3.1 18.7 + - - -
436A VAL 3.9 13.3 + - - +
437A GLY* 3.8 19.4 + - - -
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Residues in contact with TRP 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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408A ASP* 2.9 18.1 + - - +
409A TYR* 3.4 12.6 - - - +
411A ASN* 1.3 76.5 - - - +
413A ALA* 1.3 69.8 + - - +
415A GLY* 3.2 1.6 + - - -
416A HIS* 3.0 74.2 + + + +
418A VAL* 4.5 5.2 - - + -
475A ARG* 3.7 45.8 - - + -
476A VAL* 4.2 11.0 - - + -
479A TYR* 3.3 52.8 - + + +
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Residues in contact with ALA 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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409A TYR 2.9 14.5 + - - +
410A ILE 3.0 9.6 + - - +
412A TRP* 1.3 83.3 - - - +
414A ARG* 1.3 60.6 + - - +
416A HIS 3.3 5.4 + - - -
417A GLY 3.4 0.2 + - - -
418A VAL* 2.8 54.8 + - + +
420A VAL* 3.7 10.8 - - + -
468A PHE* 3.7 15.0 - - + -
476A VAL* 4.1 4.5 - - + -
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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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320A ARG* 6.3 0.7 - - - +
321A ARG* 5.0 6.0 - - - +
410A ILE* 3.1 22.6 + - - +
411A ASN* 3.8 19.0 - - - +
412A TRP 3.3 0.2 - - - -
413A ALA* 1.3 77.9 - - - +
415A GLY* 1.3 56.5 + - - +
416A HIS 3.3 3.3 + - - -
417A GLY* 3.7 7.4 + - - -
418A VAL 4.1 4.9 + - - +
420A VAL* 3.8 35.1 + - + +
421A GLY 4.8 0.6 + - - -
437A GLY* 2.7 37.1 + - - -
438A ILE 4.3 4.4 + - - -
439A THR 4.6 0.4 + - - -
440A ASN* 4.0 24.4 + - - +
646A ASP* 4.5 14.4 + - - -
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Residues in contact with GLY 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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411A ASN 3.1 15.8 + - - -
412A TRP* 3.2 2.6 + - - -
414A ARG* 1.3 75.3 - - - +
416A HIS* 1.3 75.5 + - - +
417A GLY 3.8 0.7 - - - -
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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