Contacts of the helix formed by residues 538 - 552 (chain D) 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 ASP 538 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C PHE* 4.0 13.7 - - + -
56C LYS* 4.2 0.2 - - - -
433C GLU* 3.6 11.8 + - - +
436C MET* 3.2 32.1 - - + +
437C ARG* 5.1 6.9 - - - +
537D HIS* 1.3 83.5 - - - +
539D ALA* 1.3 63.2 + - - +
540D SER* 2.9 18.4 + - - -
541D THR* 2.8 41.2 + - - -
542D ASN* 3.0 18.6 + - - -
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Residues in contact with ALA 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.7 18.4 - - + +
32C ASN 4.9 1.8 - - - +
33C LYS* 4.1 20.2 - - - +
35C ARG 4.8 0.9 - - - +
36C PHE* 3.6 30.1 - - + +
538D ASP* 1.3 74.2 - - - +
540D SER* 1.3 57.6 + - - +
542D ASN* 3.5 7.3 + - - +
543D GLY* 2.8 24.4 + - - -
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Residues in contact with SER 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C PHE* 3.5 8.9 - - - -
36C PHE* 3.8 11.0 - - - +
53C ASP* 2.5 23.4 + - - +
55C SER* 3.4 16.6 - - - -
56C LYS* 2.8 32.3 + - - +
538D ASP* 2.9 9.8 + - - -
539D ALA* 1.3 74.8 - - - +
541D THR* 1.3 56.7 + - - -
543D GLY* 2.9 2.3 + - - -
544D LEU* 2.7 37.9 + - - +
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Residues in contact with THR 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56C LYS* 4.0 10.7 + - - +
429C LEU* 4.7 7.6 + - + +
433C GLU* 3.5 18.0 - - + +
524D ILE* 4.1 15.7 - - + -
537D HIS* 3.5 35.2 - - + +
538D ASP* 2.8 31.6 + - - -
540D SER* 1.3 72.7 + - - +
542D ASN* 1.3 61.6 + - - +
544D LEU* 3.9 6.3 - - - +
545D ILE* 3.0 38.8 + - + +
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Residues in contact with ASN 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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534D VAL* 3.4 23.4 + - - +
535D THR* 3.5 14.1 - - - +
536D SER 3.7 3.4 - - - +
537D HIS* 2.8 51.4 - - - +
538D ASP 3.0 17.6 + - - +
539D ALA* 3.5 7.8 + - - +
541D THR* 1.3 75.7 - - - +
543D GLY* 1.3 56.8 + - - +
545D ILE* 3.1 7.1 + - - +
546D ASN* 2.9 37.7 + - - +
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Residues in contact with GLY 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 3.6 34.9 - - - -
539D ALA 2.8 16.1 + - - -
540D SER 3.4 2.9 - - - -
542D ASN* 1.3 74.1 - - - +
544D LEU* 1.3 61.0 + - - +
546D ASN* 3.5 8.2 + - - +
547D PHE* 3.1 24.1 + - - +
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Residues in contact with LEU 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 4.3 0.4 - - + -
51C LEU* 3.8 17.3 - - + -
53C ASP* 3.5 26.0 - - + +
56C LYS* 3.5 25.1 - - - +
428C PHE* 4.7 1.3 - - + -
429C LEU* 3.5 24.9 - - + -
432C THR* 4.7 1.8 - - - +
475C SER* 3.8 22.7 - - - +
477C VAL* 3.6 28.7 - - + -
540D SER* 2.7 19.0 + - - +
541D THR* 3.9 2.5 - - - +
543D GLY* 1.3 71.7 - - - +
545D ILE* 1.3 60.6 - - - +
547D PHE* 3.3 3.3 + - - +
548D ILE* 3.0 32.7 + - + +
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Residues in contact with ILE 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429C LEU* 3.7 20.2 - - + -
524D ILE* 4.4 17.0 - - + -
527D GLU* 4.4 2.2 - - + +
528D LEU* 4.1 13.0 - - + -
534D VAL* 3.7 44.6 - - + -
537D HIS* 4.1 7.9 - - + +
541D THR* 3.0 38.3 + - + +
542D ASN* 3.5 4.5 - - - +
544D LEU* 1.3 77.3 - - - +
546D ASN* 1.3 58.7 + - - +
548D ILE* 3.3 9.7 + - - +
549D LYS* 3.0 38.7 + - - +
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Residues in contact with ASN 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D ALA 4.7 0.2 - - - +
533D GLN* 3.4 39.3 - - - +
534D VAL* 2.9 39.8 + - - +
535D THR* 5.9 0.6 - - - +
542D ASN* 2.9 27.5 + - - +
543D GLY* 4.0 7.0 - - - +
544D LEU 3.3 0.2 - - - -
545D ILE* 1.3 77.7 - - - +
547D PHE* 1.3 57.3 + - - +
549D LYS* 3.5 6.6 + - - +
550D GLN* 3.0 28.1 + - - +
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Residues in contact with PHE 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C PHE* 5.7 0.7 - - + -
42C THR* 4.9 13.2 - - + -
49C HIS* 3.7 28.9 - + + -
50C ILE 5.1 0.2 - - - -
51C LEU* 3.4 40.8 - - + -
409C VAL* 4.4 3.4 - - + -
477C VAL* 3.6 40.2 - - + -
478C PHE* 4.6 0.7 - - - -
543D GLY 3.1 18.0 + - - +
544D LEU 3.6 3.1 - - - +
546D ASN* 1.3 75.0 - - - +
548D ILE* 1.3 60.9 + - - +
550D GLN* 3.2 20.0 + - - +
551D GLN* 2.8 55.7 + - + +
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Residues in contact with ILE 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407C ILE* 5.7 0.2 - - + -
409C VAL* 3.5 20.8 - - + +
425C LEU* 4.0 40.6 - - + -
428C PHE* 5.3 3.1 - - + -
429C LEU* 4.0 33.2 - - + -
477C VAL* 4.4 21.5 - - + -
528D LEU* 5.4 8.5 - - + -
544D LEU* 3.0 17.6 + - + +
545D ILE* 3.4 8.3 - - - +
547D PHE* 1.3 75.5 - - - +
549D LYS* 1.3 64.9 + - + +
552D ARG* 3.0 35.5 + - - +
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Residues in contact with LYS 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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527D GLU 2.8 28.4 + - - -
528D LEU* 3.7 8.3 - - + +
529D ASP 3.4 6.9 + - - -
530D GLY 3.0 25.0 + - - +
531D SER* 3.8 16.4 - - - +
532D ALA* 2.7 35.1 + - - +
533D GLN* 5.2 2.9 - - - +
534D VAL* 3.8 11.1 - - - +
545D ILE* 3.0 27.7 + - + +
546D ASN* 3.8 7.9 - - - +
548D ILE* 1.3 78.9 - - + +
550D GLN* 1.3 62.9 + - - +
552D ARG* 3.4 27.0 + - - +
553D GLU* 3.2 19.6 - - - +
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Residues in contact with GLN 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C HIS* 4.8 7.3 + - - -
546D ASN 3.0 18.6 + - - +
547D PHE* 3.2 19.8 + - - +
549D LYS* 1.3 80.1 - - - +
551D GLN* 1.3 90.7 + - - +
552D ARG 3.4 0.5 + - - -
553D GLU* 3.7 13.7 + - - +
554D ALA* 4.2 2.4 + - - +
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Residues in contact with GLN 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLY* 5.1 0.2 - - - -
49C HIS* 3.7 27.9 + - - -
409C VAL* 4.0 19.3 - - + -
410C GLN* 3.1 17.7 - - - +
479C THR* 2.7 29.2 + - + +
547D PHE* 2.8 46.6 + - + +
548D ILE 3.8 0.2 - - - -
550D GLN* 1.3 97.9 + - - +
552D ARG* 1.3 65.5 + - - +
553D GLU 3.0 4.5 + - - -
554D ALA* 3.2 28.3 + - - +
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Residues in contact with ARG 552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409C VAL* 3.9 11.7 - - + +
410C GLN* 3.5 15.2 - - + +
425C LEU* 6.2 1.4 - - - +
528D LEU* 2.7 26.5 + - - +
529D ASP* 4.7 1.6 - - - +
530D GLY 2.5 40.2 + - - +
531D SER* 4.0 3.0 - - - +
548D ILE* 3.0 25.3 + - - +
549D LYS* 3.4 28.9 + - - +
550D GLN 3.2 0.6 - - - -
551D GLN* 1.3 77.8 - - - +
553D GLU* 1.3 73.3 + - - +
555D ARG* 4.1 5.2 + - - -
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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