Contacts of the helix formed by residues 391 - 410 (chain F) in PDB entry 3IKM
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 PRO 391 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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389F ARG* 3.3 7.9 - - - +
390F GLY* 1.3 80.1 - - - +
392F THR* 1.3 71.4 + - - +
393F LEU 2.7 3.1 + - - +
394F GLU* 2.6 56.1 + - + +
395F LEU 3.6 2.6 + - - -
448F LEU* 5.7 2.7 - - + -
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Residues in contact with THR 392 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F VAL* 5.6 1.6 - - - +
389F ARG* 2.7 33.5 + - - +
390F GLY* 3.1 2.6 - - - -
391F PRO* 1.3 70.5 - - - +
393F LEU* 1.3 67.4 + - + +
395F LEU* 3.9 9.4 - - - +
396F ARG* 3.9 9.0 + - - +
420F THR* 6.5 0.9 - - + -
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Residues in contact with LEU 393 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391F PRO 2.7 5.5 + - - -
392F THR* 1.3 79.4 - - + +
394F GLU* 1.3 72.5 + - - +
395F LEU 3.0 2.9 - - - -
396F ARG* 2.5 62.9 + - + +
397F GLN* 2.9 4.3 + - - +
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Residues in contact with GLU 394 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390F GLY 4.8 0.2 - - - -
391F PRO* 2.6 58.9 + - + +
393F LEU* 1.3 84.6 - - - +
395F LEU* 1.3 57.1 + - + +
397F GLN* 2.7 53.3 + - - +
398F VAL* 3.2 6.8 - - - +
448F LEU* 4.6 15.8 - - + +
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Residues in contact with LEU 395 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387F VAL* 3.4 6.8 - - + +
388F GLY* 3.0 34.8 - - - +
389F ARG 2.8 32.5 - - - +
390F GLY 4.6 1.6 - - - +
391F PRO 4.0 2.7 - - - +
392F THR 3.9 6.3 - - - +
393F LEU 2.7 1.8 + - - -
394F GLU* 1.3 74.1 - - - +
396F ARG* 1.3 52.8 + - - +
398F VAL* 2.6 31.7 - - - +
399F CYS 2.7 13.2 + - - -
443F VAL* 2.9 16.7 - - + +
444F THR 3.1 31.9 - - - +
445F GLU* 4.5 0.2 - - - -
447F THR* 3.8 2.5 - - + -
448F LEU* 3.2 24.9 - - + -
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Residues in contact with ARG 396 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN* 3.3 36.1 - - - +
545D ALA* 5.4 2.6 - - - +
387F VAL* 3.7 16.0 - - + +
392F THR 3.9 5.5 + - - +
393F LEU* 2.5 60.0 + - + +
395F LEU* 1.3 70.1 - - - +
397F GLN* 1.3 87.0 + - - +
398F VAL 2.8 1.1 - - - -
399F CYS* 3.3 1.5 - - - +
400F GLN* 2.5 49.8 + - - +
417F TYR* 4.5 20.8 - - + -
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Residues in contact with GLN 397 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D ALA* 3.6 13.4 - - + +
548D CYS* 4.3 20.8 - - - -
549D LEU* 4.3 1.0 - - - +
552D LEU* 4.9 6.3 - - - +
393F LEU 2.9 1.7 + - - +
394F GLU* 2.7 62.3 + - - +
396F ARG* 1.3 112.2 + - - +
398F VAL* 1.3 63.7 + - + +
400F GLN* 3.2 9.4 - - - +
401F GLY* 2.9 21.5 + - - -
448F LEU* 5.7 2.8 - - - +
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Residues in contact with VAL 398 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LEU* 3.3 27.7 - - + +
552D LEU* 4.0 11.9 - - + -
394F GLU 3.2 17.9 - - - +
395F LEU* 2.6 16.8 + - - +
397F GLN* 1.3 83.1 - - + +
399F CYS* 1.3 52.5 + - - +
401F GLY* 2.6 21.7 + - - -
402F LEU* 2.7 38.7 + - + +
443F VAL* 4.4 9.0 - - + -
447F THR* 5.4 10.3 - - + +
448F LEU* 5.7 5.4 - - + -
468F ILE* 6.2 1.3 - - + -
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Residues in contact with CYS 399 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385F LEU* 2.9 31.5 - - - +
386F ASP 4.8 0.7 - - - -
387F VAL* 3.2 28.9 - - + +
395F LEU 2.7 9.3 + - - -
396F ARG* 3.3 7.0 - - - +
398F VAL* 1.3 69.1 - - - +
400F GLN* 1.3 68.7 + - - +
402F LEU* 3.0 6.5 + - - +
403F PHE* 2.7 23.9 + - - +
417F TYR* 3.0 53.6 - - + -
443F VAL* 4.5 0.9 - - + -
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Residues in contact with GLN 400 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541D GLN* 4.6 12.8 - - + +
542D ASP* 3.9 13.0 + - - +
545D ALA* 2.8 32.2 - - + +
546D ARG* 4.1 4.2 + - - +
396F ARG* 2.5 34.6 + - - +
397F GLN 3.2 9.9 - - - +
399F CYS* 1.3 71.8 - - - +
401F GLY* 1.3 72.8 + - - +
403F PHE* 3.3 0.3 - - - +
404F ASN* 2.5 64.7 + - - +
417F TYR* 3.9 19.0 - - + -
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Residues in contact with GLY 401 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546D ARG* 4.5 7.2 + - - -
549D LEU* 3.2 21.3 - - - -
397F GLN 2.9 4.1 + - - -
398F VAL 2.6 14.5 + - - -
400F GLN* 1.3 88.2 + - - +
402F LEU* 1.3 67.7 + - - +
404F ASN* 3.7 0.5 - - - +
405F GLU* 2.7 23.9 + - - +
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Residues in contact with LEU 402 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D LEU* 3.7 17.7 - - + -
553D LYS* 4.8 4.3 - - - +
385F LEU* 3.1 34.3 - - + -
398F VAL* 2.7 24.1 + - + +
399F CYS 3.5 0.4 - - - +
401F GLY* 1.3 71.5 - - - +
403F PHE* 1.3 56.8 + - - +
405F GLU* 4.2 1.3 - - - -
406F LEU* 2.4 50.8 + - + +
441F VAL* 4.8 1.6 - - + -
443F VAL* 4.2 20.6 - - + -
468F ILE* 4.1 28.0 - - + -
472F LYS* 3.0 25.6 - - - +
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Residues in contact with PHE 403 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL 3.1 18.4 - - - -
121E PHE 2.8 24.2 - - - -
122E ARG* 5.3 0.4 - - - -
123E GLU* 3.2 23.3 - - + -
385F LEU* 3.1 10.3 - - + +
399F CYS 2.7 11.6 + - - +
400F GLN 3.3 7.0 - - - +
402F LEU* 1.3 74.9 - - - +
404F ASN* 1.3 61.6 + - - +
406F LEU* 2.7 7.6 + - - +
407F LEU* 2.3 51.4 + - + -
413F VAL* 5.3 7.6 - - + -
415F PRO* 3.0 37.5 - - + -
417F TYR* 2.4 35.7 - + + +
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Residues in contact with ASN 404 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538D GLU* 3.7 2.8 + - - -
542D ASP* 2.4 29.9 + - - -
546D ARG* 2.6 24.7 - - - +
121E PHE* 5.3 5.1 + - - +
400F GLN* 2.5 38.4 + - - +
401F GLY 3.7 0.2 - - - +
403F PHE* 1.3 90.5 - - - +
405F GLU* 1.3 67.4 + - - +
406F LEU 2.8 0.9 + - - -
407F LEU* 2.9 8.0 + - - +
408F GLU* 2.6 35.1 + - - +
417F TYR* 4.9 0.5 + - - -
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Residues in contact with GLU 405 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546D ARG* 3.8 10.6 - - + +
549D LEU* 5.7 1.8 - - + -
553D LYS* 4.7 18.5 + - - +
401F GLY 2.7 25.1 + - - +
402F LEU* 3.2 3.4 - - - +
404F ASN* 1.3 74.1 - - - +
406F LEU* 1.3 65.7 + - + +
408F GLU* 3.3 10.3 + - - +
409F ASN* 2.4 55.4 + - - +
472F LYS* 5.4 5.4 - - - +
473F ASP* 4.3 14.5 - - - +
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Residues in contact with LEU 406 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383F VAL* 5.3 3.8 - - + -
385F LEU* 3.9 15.3 - - + -
402F LEU* 2.4 44.7 + - + +
403F PHE* 2.7 13.6 + - - +
405F GLU* 1.3 84.8 - - + +
407F LEU* 1.3 64.9 + - - +
408F GLU 2.7 2.6 + - - -
409F ASN* 2.6 32.9 + - - +
411F ILE* 3.0 31.1 - - + +
413F VAL* 4.0 14.4 - - + -
472F LYS* 3.6 31.0 - - + +
475F LEU* 5.7 2.2 - - + -
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Residues in contact with LEU 407 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL* 2.8 61.2 - - + +
121E PHE* 3.4 24.9 - - + -
403F PHE* 2.3 44.2 + - + +
404F ASN* 3.2 13.9 - - - +
406F LEU* 1.3 67.9 - - - +
408F GLU* 1.3 89.2 + - + +
410F GLY* 3.7 7.4 + - - -
411F ILE* 4.1 15.1 + - - +
413F VAL* 4.8 2.6 - - - +
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Residues in contact with GLU 408 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D GLU* 4.7 9.0 - - - +
546D ARG* 2.4 50.4 + - - +
121E PHE* 6.1 0.5 - - - -
404F ASN 2.6 29.6 + - - +
405F GLU* 3.3 7.2 + - - +
406F LEU 2.7 3.8 + - - -
407F LEU* 1.3 99.0 - - + +
409F ASN* 1.3 68.9 + - - +
410F GLY* 2.8 6.3 + - - -
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Residues in contact with ASN 409 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405F GLU* 2.4 34.3 + - - +
406F LEU* 2.6 41.0 + - - +
408F GLU* 1.3 72.6 - - - +
410F GLY* 1.3 55.6 + - - +
411F ILE* 3.7 9.8 - - + +
473F ASP* 6.1 0.9 - - - -
476F ILE* 5.8 11.4 - - + -
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Residues in contact with GLY 410 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407F LEU 4.2 4.0 - - - -
408F GLU 2.8 10.3 + - - -
409F ASN* 1.3 77.0 - - - +
411F ILE* 1.3 61.4 + - - +
412F SER 4.4 0.3 + - - -
479F ILE* 4.7 10.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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