Contacts of the helix formed by residues 514 - 529 (chain C) in PDB entry 1JLH
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 514 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357C GLU* 4.4 17.0 - - - +
511C GLN* 3.4 26.9 - - + +
512C TRP 3.0 2.4 + - - -
513C GLY* 1.3 79.1 - - - +
515C GLU* 1.3 69.4 + - + +
516C LEU 3.7 0.2 - - - -
517C GLY* 4.2 2.9 + - - -
518C LYS* 3.7 21.6 + - + +
387D GLN 5.1 10.1 - - - +
388D HIS* 6.2 1.1 - - - +
391D TYR* 5.6 2.7 - - + -
392D GLN* 4.5 18.2 - - + +
395D HIS* 5.9 1.3 - - - -
431D GLN* 5.5 1.4 + - - -
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Residues in contact with GLU 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C GLN 5.2 0.2 - - - +
512C TRP* 3.3 44.3 + - + +
514C VAL* 1.3 83.4 - - + +
516C LEU* 1.3 69.6 + - - +
518C LYS* 3.1 7.9 + - - +
519C GLN* 2.9 40.0 + - + +
439D LYS* 5.3 1.8 + - - +
465D LYS* 3.2 32.8 + - - +
467D PHE* 4.7 3.7 - - + -
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Residues in contact with LEU 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C VAL 3.7 0.2 - - - -
515C GLU* 1.3 76.8 - - - +
517C GLY* 1.3 65.1 + - - +
519C GLN* 3.0 16.7 + - + +
520C LEU* 3.0 48.9 + - + +
434D ALA* 3.7 22.4 - - + +
437D ARG* 5.3 1.8 - - - +
438D GLY* 3.5 42.2 - - - +
439D LYS* 4.4 15.3 - - - -
467D PHE* 3.6 36.0 - - + -
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Residues in contact with GLY 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C GLY 5.3 0.2 + - - -
514C VAL 4.2 3.7 + - - -
515C GLU 3.3 1.0 - - - -
516C LEU* 1.3 79.5 - - - +
518C LYS* 1.3 61.6 + - - +
520C LEU* 4.9 0.2 - - - -
521C ALA* 3.1 23.2 + - - +
395D HIS* 4.9 3.4 + - - -
427D ASN* 5.0 1.1 - - - +
430D ALA* 3.5 9.1 - - - +
431D GLN* 3.5 28.0 + - - -
434D ALA* 4.0 17.5 - - - +
467D PHE* 5.3 0.4 - - - -
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Residues in contact with LYS 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C THR 5.8 0.6 + - - -
214C THR* 5.6 7.9 - - - +
215C GLN* 5.5 21.0 - - - +
216C GLU* 5.6 6.3 + - - +
514C VAL* 3.7 16.4 + - + +
515C GLU* 3.1 10.8 + - - +
517C GLY* 1.3 76.1 - - - +
519C GLN* 1.3 63.4 + - + +
521C ALA* 3.4 7.0 + - + +
522C LYS* 3.3 28.6 + - + +
387D GLN* 6.1 0.2 - - - -
427D ASN* 5.3 3.4 - - - +
431D GLN* 4.4 1.4 - - - +
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Residues in contact with GLN 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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515C GLU* 2.9 29.3 + - + +
516C LEU* 3.2 31.8 - - - +
518C LYS* 1.3 77.6 - - + +
520C LEU* 1.3 69.1 + - + +
521C ALA 3.3 0.7 + - - -
522C LYS* 3.3 16.0 + - - +
523C LYS* 3.5 18.4 + - - +
439D LYS* 2.8 25.3 + - - +
447D GLU* 3.0 25.0 - - - +
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Residues in contact with LEU 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 3.0 35.5 + - + +
517C GLY 4.1 0.4 - - - +
519C GLN* 1.3 78.9 - - + +
521C ALA* 1.3 62.4 + - - +
523C LYS* 3.4 31.3 + - - +
524C ILE* 3.2 26.3 + - - +
537C HIS* 5.3 0.6 - - + -
430D ALA* 3.6 12.1 - - + +
433D GLU* 3.5 34.0 - - + +
434D ALA* 3.6 29.2 - - + +
437D ARG* 4.5 14.6 - - - +
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Residues in contact with ALA 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLN* 6.0 1.3 - - - +
517C GLY 3.1 18.4 + - - +
518C LYS* 3.5 7.9 - - + +
519C GLN 3.2 0.4 - - - -
520C LEU* 1.3 74.7 - - - +
522C LYS* 1.3 66.8 + - + +
524C ILE* 3.2 2.2 + - - +
525C GLU* 3.0 31.7 + - - +
426D ALA* 3.8 8.9 - - + +
427D ASN* 4.0 29.6 - - - +
430D ALA* 3.3 15.4 - - + +
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLN* 3.5 19.9 + - - +
518C LYS* 3.3 18.5 + - + +
519C GLN* 3.3 10.1 + - - +
521C ALA* 1.3 79.6 - - + +
523C LYS* 1.3 59.5 + - + +
525C GLU* 3.0 43.1 + - - +
526C PRO* 3.0 23.7 - - - +
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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
----------------------------------------------------------
519C GLN* 3.5 12.5 + - - +
520C LEU* 3.4 34.6 + - - +
521C ALA 3.2 0.6 - - - -
522C LYS* 1.3 80.0 - - + +
524C ILE* 1.3 58.9 + - - +
526C PRO* 3.2 21.5 - - - +
527C GLU* 3.6 14.3 - - - +
537C HIS* 5.2 10.5 - - + -
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Residues in contact with ILE 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 LEU 3.2 15.3 + - - +
521C ALA 3.2 4.0 + - - +
523C LYS* 1.3 76.6 - - - +
525C GLU* 1.3 67.4 + - - +
527C GLU* 2.9 19.2 + - - +
528C LEU* 3.2 19.0 + - + +
537C HIS* 3.7 20.2 - - + +
541C THR* 4.3 8.7 - - + -
545C ILE* 4.3 9.6 - - + -
426D ALA* 4.1 9.2 - - + +
429D LEU* 3.9 29.8 - - + -
430D ALA* 3.7 26.0 - - + +
433D GLU* 3.6 20.6 - - - +
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Residues in contact with GLU 525 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C GLN* 3.0 18.9 + - - +
521C ALA* 3.0 22.3 + - - +
522C LYS* 3.0 37.5 + - - +
524C ILE* 1.3 76.5 - - - +
526C PRO* 1.3 68.7 - - + +
528C LEU* 3.2 12.0 + - - +
529C ASP* 3.7 0.2 - - - +
422D LYS* 2.9 33.5 + - - +
423D ILE* 3.4 30.4 - - + +
426D ALA* 3.6 19.6 - - + +
427D ASN* 5.0 0.3 + - - -
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Residues in contact with PRO 526 (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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522C LYS 3.0 27.4 - - - +
523C LYS* 3.2 18.2 - - - +
525C GLU* 1.3 83.9 - - + +
527C GLU* 1.3 61.6 + - + +
528C LEU 3.3 0.9 + - - -
529C ASP* 3.3 23.3 + - - +
422D LYS* 4.5 7.0 - - - +
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Residues in contact with GLU 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 3.6 16.2 - - - +
524C ILE* 2.9 14.6 + - - +
526C PRO* 1.3 77.0 - - + +
528C LEU* 1.3 60.8 + - - +
529C ASP 3.2 2.9 + - - +
534C VAL* 4.0 19.4 - - + +
536C SER* 2.5 28.9 + - - -
537C HIS* 2.4 31.4 + - - -
545C ILE* 4.3 4.9 - - + +
549C LYS* 2.8 29.3 + - - -
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Residues in contact with LEU 528 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524C ILE* 3.2 13.4 + - + +
525C GLU* 3.2 9.4 + - - +
526C PRO 3.2 1.2 - - - -
527C GLU* 1.3 75.3 - - - +
529C ASP* 1.3 66.8 + - - +
530C GLY 3.6 0.9 - - - +
545C ILE* 4.3 17.7 - - + +
548C ILE* 5.0 15.3 - - + -
549C LYS* 3.7 4.1 - - + +
552C ARG* 2.6 37.8 + - - +
422D LYS* 3.4 39.0 - - + +
425D LEU* 4.1 11.2 - - + -
426D ALA* 3.9 21.5 - - + +
429D LEU* 4.2 20.4 - - + -
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Residues in contact with ASP 529 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526C PRO* 3.6 17.9 - - - +
527C GLU* 3.2 8.7 - - - +
528C LEU* 1.3 79.6 - - - +
530C GLY* 1.3 60.6 + - - +
532C ALA* 5.9 0.5 - - - +
549C LYS* 3.6 2.1 + - - -
552C ARG* 4.8 0.7 - - - +
422D LYS* 2.9 42.5 + - - +
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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
------------------------------------------------------------
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