Contacts of the helix formed by residues 520 - 529 (chain A) in PDB entry 2JGN
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 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518A PRO* 3.4 4.9 - - - +
519A SER* 1.3 92.0 + - - +
521A ILE* 1.3 65.9 + - - +
522A GLU* 3.3 15.3 - - - +
523A GLU* 3.2 30.8 + - - +
524A TYR 3.3 8.3 + - - -
551A ILE* 3.5 7.9 - - - -
554A ASP* 5.9 0.9 - - - -
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Residues in contact with ILE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A ASP* 1.3 72.6 - - - +
522A GLU* 1.3 69.8 + - - +
524A TYR* 3.2 21.9 + - + +
525A VAL* 2.8 39.4 + - + +
551A ILE* 3.6 13.5 - - + +
554A ASP* 3.8 32.1 + - + +
555A LEU* 3.7 29.8 - - + +
558A LEU* 3.5 30.7 - - + -
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Residues in contact with GLU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A ASP* 3.7 14.5 - - - +
521A ILE* 1.3 96.8 + - + +
523A GLU* 1.3 57.8 + - - +
525A VAL* 3.2 10.2 + - - +
526A HIS* 3.0 26.3 + - - +
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Residues in contact with GLU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 5.9 0.2 - - - -
498A ALA* 4.7 18.1 - - + +
518A PRO* 3.6 21.3 - - + -
520A ASP* 3.2 24.7 + - - +
522A GLU* 1.3 77.7 - - - +
524A TYR* 1.3 64.5 + - - +
526A HIS* 3.3 20.5 + - - +
527A ARG* 3.1 54.1 + - - +
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Residues in contact with TYR 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A GLN* 2.7 43.0 + - - +
418A VAL* 4.7 2.9 - - - +
514A ASN* 3.7 7.0 - - - -
517A LEU* 3.7 21.5 - - + -
518A PRO* 3.5 15.0 - - + +
520A ASP 3.3 3.8 + - - -
521A ILE* 3.2 24.6 + - + +
523A GLU* 1.3 76.5 - - - +
525A VAL* 1.3 63.2 + - - +
527A ARG* 3.2 4.8 + - - +
528A ILE* 3.0 48.4 + - + +
540A ALA* 5.2 1.4 + - - +
542A SER* 3.3 25.7 + - - -
551A ILE* 4.5 3.1 - - + -
555A LEU* 3.9 19.1 - - + +
558A LEU* 3.7 27.6 - - + -
559A LEU* 4.5 1.0 - - - +
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Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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521A ILE* 2.8 23.8 + - + +
522A GLU* 3.2 11.2 + - - +
524A TYR* 1.3 73.7 - - + +
526A HIS* 1.3 65.3 + - - +
528A ILE* 3.6 12.3 + - + +
529A GLY* 3.1 20.6 + - - -
558A LEU* 3.8 24.0 - - + -
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Residues in contact with HIS 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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522A GLU 3.0 13.6 + - - +
523A GLU* 3.6 27.1 - - - +
525A VAL* 1.3 80.6 - - - +
527A ARG* 1.3 61.2 + - + +
529A GLY* 3.5 8.1 + - - -
530A ARG* 3.5 40.4 + - - +
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Residues in contact with ARG 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446A PHE* 3.5 47.6 - - + +
447A VAL 4.6 13.9 + - - -
448A GLU* 5.1 7.3 + - - +
498A ALA* 5.0 11.3 - - - +
512A VAL* 3.8 10.8 - - - +
514A ASN* 3.2 26.9 + - - +
516A ASP 2.7 28.5 + - - -
517A LEU 4.3 0.8 + - - -
518A PRO* 3.6 35.2 - - - +
523A GLU* 3.1 41.1 + - - +
524A TYR* 3.7 3.8 - - - +
526A HIS* 1.3 75.3 - - + +
528A ILE* 1.3 66.5 + - - +
530A ARG* 3.2 23.0 + - - +
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Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A SER* 3.9 18.6 - - - +
414A ILE* 3.4 16.2 - - + +
416A GLN* 3.7 33.7 - - + +
512A VAL* 4.5 5.8 - - + -
514A ASN* 3.8 11.0 - - - +
524A TYR* 3.0 54.6 + - + +
525A VAL* 3.6 15.7 - - + +
527A ARG* 1.3 77.3 - - - +
529A GLY* 1.3 56.7 + - - +
530A ARG 3.1 5.7 + - - -
531A THR* 3.2 21.4 - - - +
540A ALA* 3.6 26.9 - - + -
558A LEU* 5.1 1.1 - - + -
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Residues in contact with GLY 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ILE* 4.3 9.2 - - - -
507A SER* 5.1 4.2 - - - -
508A ASN 5.1 1.2 + - - -
525A VAL 3.1 16.0 + - - -
526A HIS* 3.5 4.5 + - - -
527A ARG 3.1 1.8 - - - -
528A ILE* 1.3 75.4 - - - +
530A ARG* 1.3 61.2 + - - +
531A THR 3.2 9.3 + - - +
532A GLY 4.7 3.3 - - - +
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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