Contacts of the helix formed by residues 514 - 523 (chain D) in PDB entry 2JAZ
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 SER 514 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54C ILE 4.2 2.9 - - - -
55C TYR* 2.7 35.4 + - - -
56C TYR* 4.9 0.8 - - - -
57C PRO* 3.5 23.3 - - - -
63C ASP* 3.5 7.2 - - - -
513D PHE* 1.3 77.2 - - - +
515D ARG* 1.3 66.3 + - - +
516D ASN 3.8 2.9 + - - -
517D ASN* 3.2 19.3 + - - +
518D ASN* 3.0 21.2 + - - +
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Residues in contact with ARG 515 (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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64A SER* 5.8 0.9 - - - -
66A GLU* 5.3 0.2 - - - +
515B ARG* 2.8 72.4 - - - +
62C ASP* 5.7 2.8 - - - +
63C ASP* 2.7 59.3 + - - +
64C SER* 3.7 14.7 - - - +
65C PRO* 5.7 0.4 - - - +
514D SER* 1.3 70.6 - - - +
516D ASN* 1.3 66.8 + - - +
518D ASN* 3.3 8.8 + - - +
519D ASP* 3.1 29.8 + - - +
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Residues in contact with ASN 516 (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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22C ILE* 4.5 4.9 - - - +
23C GLU* 3.6 33.7 - - - +
26C ASN* 2.8 24.8 + - - +
54C ILE* 3.3 36.4 - - + +
55C TYR* 3.6 17.3 - - + -
63C ASP* 4.7 4.7 + - - +
68C ILE* 5.4 4.0 - - - +
514D SER* 3.3 1.8 + - - +
515D ARG* 1.3 83.6 - - - +
517D ASN* 1.3 62.0 + - - +
519D ASP* 3.5 10.0 + - - +
520D ARG* 3.3 23.7 + - - +
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Residues in contact with ASN 517 (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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55C TYR* 3.5 31.3 + - - +
56C TYR* 3.6 10.7 + - - -
513D PHE* 4.1 15.2 - - + -
514D SER* 3.2 14.6 + - - +
516D ASN* 1.3 76.1 - - - +
518D ASN* 1.3 65.1 + - - +
520D ARG* 3.2 12.9 + - - +
521D MET* 3.1 27.6 + - - +
527D PRO* 3.3 19.6 - - + +
528D LYS 2.7 40.8 + - - -
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Residues in contact with ASN 518 (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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66A GLU* 3.7 16.9 - - + +
504D SER* 4.0 10.4 + - - +
510D SER* 3.0 48.3 - - - +
513D PHE* 3.2 15.8 - - - +
514D SER 3.0 13.2 + - - +
515D ARG* 3.7 7.1 - - - +
517D ASN* 1.3 76.7 - - - +
519D ASP* 1.3 57.4 + - - +
521D MET* 3.2 23.1 + - - +
522D LYS* 2.8 30.8 + - - +
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Residues in contact with ASP 519 (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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16A VAL* 4.8 1.3 - - - +
20A LYS* 3.0 29.6 + - - -
65A PRO* 3.7 14.6 - - - +
66A GLU* 2.6 35.9 - - - +
23C GLU* 4.6 4.5 - - - +
26C ASN* 4.9 5.1 - - + +
27C VAL* 3.7 29.7 - - + +
515D ARG* 3.1 17.9 + - - +
516D ASN* 3.6 12.4 - - - +
518D ASN* 1.3 78.3 - - - +
520D ARG* 1.3 63.7 + - - +
522D LYS* 3.4 9.4 + - - +
523D VAL* 3.4 8.5 + - - +
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Residues in contact with ARG 520 (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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26C ASN* 3.4 34.4 + - - +
31C ASP* 2.9 40.6 + - - -
34C LEU* 3.1 20.8 - - - +
55C TYR* 3.9 8.1 - - - -
516D ASN 3.3 6.3 + - - +
517D ASN* 3.2 28.1 + - - +
519D ASP* 1.3 77.3 - - - +
521D MET* 1.3 64.0 + - - +
523D VAL* 3.0 13.7 + - - +
525D LYS* 3.0 42.6 + - + +
526D ALA 2.8 30.8 + - - +
527D PRO* 4.7 0.4 - - + -
528D LYS* 3.7 14.8 - - - +
540D SER* 4.2 12.1 + - - -
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Residues in contact with MET 521 (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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500D TRP* 3.4 33.8 - - + +
501D GLU* 3.3 17.2 + - - -
503D VAL* 3.6 28.3 - - + -
504D SER* 3.9 6.1 - - - -
510D SER* 4.8 0.9 - - - -
513D PHE* 3.7 28.0 - - + -
517D ASN 3.1 8.2 + - - +
518D ASN* 3.2 38.1 - - - +
520D ARG* 1.3 76.4 - - - +
522D LYS* 1.3 58.0 + - - +
524D GLY 2.8 16.6 + - - -
525D LYS 3.2 8.3 - - - +
527D PRO* 3.8 27.4 - - + -
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Residues in contact with LYS 522 (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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12A GLU* 2.7 41.7 + - - +
13A ALA* 4.4 6.9 - - - +
16A VAL* 3.7 29.8 - - + -
66A GLU* 3.5 32.7 + - + +
69A VAL* 4.7 9.6 - - - +
501D GLU* 3.8 13.3 - - + +
504D SER* 3.5 17.9 - - - +
505D LYS* 4.2 20.8 - - - +
518D ASN 2.8 17.4 + - - +
519D ASP* 3.5 6.5 - - - +
520D ARG 3.2 0.2 - - - -
521D MET* 1.3 77.6 - - - +
523D VAL* 1.3 59.7 + - + +
524D GLY 3.6 0.5 + - - -
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Residues in contact with VAL 523 (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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13A ALA* 3.9 37.5 - - + +
16A VAL* 4.5 6.3 - - + -
17A GLN* 4.9 0.9 - - + -
27C VAL* 3.8 46.2 - - + +
28C ALA 4.5 2.0 - - - +
29C ALA* 6.2 0.2 - - - -
497D LYS* 4.4 9.0 - - - +
501D GLU* 3.8 8.0 - - - +
519D ASP 3.4 9.4 + - - +
520D ARG 3.0 16.9 + - - +
522D LYS* 1.3 79.4 - - - +
524D GLY* 1.3 59.2 + - - +
525D LYS* 4.2 17.4 - - + +
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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