Contacts of the helix formed by residues 515 - 529 (chain C) in PDB entry 1JIQ
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 VAL 515 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358C GLU* 3.9 21.1 - - - +
512C GLN* 3.3 30.7 - - + +
513C TRP 3.0 1.6 + - - -
514C GLY* 1.3 81.5 - - - +
516C GLU* 1.3 68.1 + - + +
517C LEU 3.5 1.2 + - - -
518C GLY* 3.8 3.5 + - - -
519C LYS* 3.4 41.0 + - + +
388D GLN 5.5 6.7 - - - +
389D HIS* 6.5 0.4 - - - -
392D TYR* 6.2 1.1 - - + -
393D GLN* 4.3 12.3 - - + +
396D HIS* 6.1 0.7 - - - -
432D GLN* 5.3 2.3 + - - -
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Residues in contact with GLU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C TRP* 3.3 26.8 + - - +
514C GLY 3.4 0.4 - - - -
515C VAL* 1.3 81.5 - - + +
517C LEU* 1.3 66.0 + - - +
519C LYS* 3.2 8.5 + - + +
520C GLN* 3.0 44.3 + - + +
440D LYS* 4.8 5.0 + - - +
466D LYS* 2.7 37.9 + - - +
468D PHE* 4.6 3.8 - - + -
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515C VAL 3.5 1.0 - - - -
516C GLU* 1.3 77.1 - - - +
518C GLY* 1.3 64.6 + - - +
520C GLN* 3.1 13.6 + - - +
521C LEU* 2.9 44.8 + - + +
396D HIS* 5.4 0.2 - - + -
435D ALA* 3.7 27.8 - - + +
439D GLY* 3.5 42.4 - - - +
440D LYS* 3.8 20.4 - - + +
468D PHE* 3.6 38.4 - - + -
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Residues in contact with GLY 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C GLY 5.5 0.2 + - - -
515C VAL 3.8 4.9 + - - -
516C GLU 3.4 0.4 - - - -
517C LEU* 1.3 77.9 - - - +
519C LYS* 1.3 56.8 + - - +
521C LEU* 4.6 0.7 - - - -
522C ALA* 3.0 31.0 + - - +
396D HIS* 5.1 3.6 + - - -
428D ASN* 4.8 1.8 - - - +
431D ALA* 3.8 7.6 - - - +
432D GLN* 3.6 28.8 + - - -
435D ALA* 4.1 15.6 - - - +
468D PHE* 5.4 0.2 - - - -
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Residues in contact with LYS 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C ILE* 4.4 12.3 - - - +
215C THR* 5.0 6.5 - - - +
216C GLN 5.9 1.2 - - - +
515C VAL* 3.4 34.4 + - + +
516C GLU* 3.2 10.6 + - + +
518C GLY* 1.3 73.4 - - - +
520C GLN* 1.3 66.4 + - + +
522C ALA* 3.5 4.9 + - - +
523C LYS* 3.2 23.2 + - - +
388D GLN* 5.9 2.9 - - - +
389D HIS* 4.1 27.8 + - - -
428D ASN* 5.5 3.8 - - - +
432D GLN* 5.9 1.1 - - - +
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Residues in contact with GLN 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516C GLU* 3.0 27.5 + - + +
517C LEU* 3.5 18.1 - - - +
519C LYS* 1.3 76.3 - - + +
521C LEU* 1.3 69.5 + - + +
523C LYS* 3.3 15.4 + - - +
524C LYS* 3.4 18.8 + - + +
440D LYS* 2.7 29.9 + - - +
448D GLU* 3.0 28.7 + - - -
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Residues in contact with LEU 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517C LEU* 2.9 33.4 + - + +
518C GLY 4.2 0.2 - - - +
520C GLN* 1.3 79.4 - - + +
522C ALA* 1.3 64.6 + - - +
524C LYS* 3.3 20.1 + - + +
525C ILE* 3.2 26.0 + - - +
538C HIS* 5.4 0.2 - - - -
431D ALA* 3.5 15.3 - - + +
434D GLU* 3.7 28.7 - - + +
435D ALA* 3.7 35.4 - - + +
438D ARG* 5.3 4.9 - - + -
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Residues in contact with ALA 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLN* 6.1 0.2 - - - +
518C GLY 3.0 19.3 + - - +
519C LYS* 4.0 4.5 - - - +
520C GLN 3.3 0.2 - - - -
521C LEU* 1.3 74.9 - - - +
523C LYS* 1.3 64.4 + - - +
525C ILE* 3.2 3.5 + - - +
526C GLU* 3.0 31.7 + - - +
427D ALA* 3.7 15.6 - - + +
428D ASN* 3.9 26.9 - - - +
431D ALA* 3.2 16.0 - - + +
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Residues in contact with LYS 523 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216C GLN* 2.9 24.1 - - - +
519C LYS 3.2 12.9 + - - +
520C GLN* 3.6 11.2 - - - +
521C LEU 3.2 0.2 - - - -
522C ALA* 1.3 80.3 - - - +
524C LYS* 1.3 61.0 + - + +
526C GLU* 2.5 34.4 + - - +
527C PRO* 3.3 20.1 - - - +
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Residues in contact with LYS 524 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520C GLN* 3.4 14.1 + - + +
521C LEU* 3.3 24.1 + - + +
522C ALA 3.3 0.6 - - - -
523C LYS* 1.3 76.7 - - + +
525C ILE* 1.3 62.3 + - - +
527C PRO* 3.3 17.7 - - - +
528C GLU* 3.5 19.2 + - - +
537C SER* 6.2 2.2 - - - -
538C HIS* 5.1 12.3 - - + -
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Residues in contact with ILE 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521C LEU 3.2 13.0 + - - +
522C ALA 3.2 3.9 + - - +
524C LYS* 1.3 81.0 - - - +
526C GLU* 1.3 67.7 + - - +
528C GLU* 2.9 23.8 + - - +
529C LEU* 3.4 12.9 + - + +
538C HIS* 3.5 25.6 - - + +
542C THR* 4.2 7.2 - - + -
546C ILE* 4.6 4.5 - - + -
427D ALA* 3.6 25.6 - - + -
430D LEU* 3.9 21.3 - - + -
431D ALA* 3.9 22.2 - - + +
434D GLU* 3.6 22.4 - - - +
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Residues in contact with GLU 526 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C GLN* 2.9 26.5 + - - +
522C ALA* 3.0 19.8 + - - +
523C LYS* 2.5 36.5 + - - +
525C ILE* 1.3 76.8 - - - +
527C PRO* 1.3 70.7 - - + +
528C GLU 3.1 0.3 + - - -
529C LEU* 3.1 17.9 + - - +
530C ASP* 4.2 0.2 - - - +
423D LYS* 3.9 25.1 - - + +
424D ILE* 3.9 22.0 - - - +
427D ALA* 3.5 17.9 - - + +
428D ASN* 4.7 2.6 + - - -
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Residues in contact with PRO 527 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523C LYS* 3.3 13.2 - - - +
524C LYS* 3.3 15.3 - - - +
526C GLU* 1.3 95.4 - - + +
528C GLU* 1.3 61.9 + - + +
529C LEU 3.4 0.3 + - - -
530C ASP* 3.7 25.6 + - - +
423D LYS* 5.7 0.4 - - - +
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Residues in contact with GLU 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524C LYS* 3.5 21.2 + - - +
525C ILE* 2.9 17.3 + - - +
527C PRO* 1.3 79.4 - - + +
529C LEU* 1.3 59.4 + - - +
530C ASP 3.4 2.5 - - - +
535C VAL* 3.7 19.8 - - + +
537C SER* 2.5 30.8 + - - -
538C HIS* 2.6 29.2 + - - -
546C ILE* 4.4 4.5 - - + +
550C LYS* 2.9 26.5 + - - -
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Residues in contact with LEU 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C ILE* 3.8 13.2 - - + +
526C GLU 3.1 8.3 + - - +
528C GLU* 1.3 75.3 - - - +
530C ASP* 1.3 63.1 + - - +
546C ILE* 4.1 27.1 - - + -
549C ILE* 5.0 11.9 - - + -
550C LYS* 3.4 7.4 + - + +
553C ARG* 2.7 35.3 + - - +
423D LYS* 3.5 41.3 - - + +
426D LEU* 3.9 19.3 - - + -
427D ALA* 4.0 13.2 - - + +
430D LEU* 4.1 18.2 - - + -
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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