Contacts of the strand formed by residues 443 - 447 (chain C) 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 THR 443 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434C LEU* 4.2 12.9 - - + +
437C THR* 6.2 0.2 - - - +
441C SER* 3.7 10.6 + - - -
442C LEU* 1.3 76.2 + - - +
444C LEU* 1.3 60.8 + - - +
445C VAL* 4.0 12.1 - - + -
486C PHE* 3.2 6.4 - - - -
492C PRO 2.9 9.3 + - - -
493C ILE* 3.4 13.7 - - + +
494C LEU 3.0 24.9 + - - +
511C HIS* 3.3 22.8 + - + +
513C ILE* 3.5 32.8 - - + -
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Residues in contact with LEU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C LEU 4.2 0.4 - - - -
443C THR* 1.3 72.7 - - - +
445C VAL* 1.3 61.4 + - - +
446C PHE* 3.6 32.7 + - + -
486C PHE* 4.4 5.8 - - + -
494C LEU* 3.5 37.2 - - + +
496C ALA* 4.1 5.4 - - + -
504C LEU* 3.9 17.5 - - + -
506C ILE* 4.1 15.5 - - + -
509C VAL* 4.3 9.6 - - + +
511C HIS 3.0 9.6 + - - +
512C VAL* 3.4 6.8 - - + +
513C ILE* 2.8 26.5 + - - +
530C ARG* 3.9 29.8 - - + -
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Residues in contact with VAL 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 4.5 10.1 - - + -
434C LEU* 5.4 0.4 - - + -
443C THR* 4.0 14.4 - - + -
444C LEU* 1.3 78.6 - - - +
446C PHE* 1.3 64.4 + - - +
447C VAL* 4.5 1.1 - - + -
456C LEU* 3.8 21.1 - - + -
460C LEU* 5.4 1.1 - - + -
493C ILE* 3.9 24.7 - - + -
494C LEU 2.8 9.8 + - - +
495C VAL* 3.3 10.0 - - + +
496C ALA* 2.8 26.2 + - - +
513C ILE* 3.4 19.3 - - + +
515C PHE* 3.7 28.5 - - + -
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Residues in contact with PHE 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C LEU* 3.6 34.3 - - + -
445C VAL* 1.3 74.2 - - - +
447C VAL* 1.3 59.7 - - - +
496C ALA* 3.4 30.1 - - + -
497C THR 4.2 3.1 - - - -
501C ALA* 3.6 24.2 - - + -
504C LEU* 3.9 10.1 - - + -
512C VAL* 3.9 15.7 - - + -
513C ILE 2.9 9.0 + - - +
514C ASN* 3.8 11.7 - - - +
515C PHE* 2.9 27.2 + - - +
516C ASP 3.2 6.8 + - - +
527C ARG* 3.5 59.0 - - + +
530C ARG* 4.2 7.0 - - - -
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Residues in contact with VAL 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C VAL* 4.5 0.7 - - + -
446C PHE* 1.3 78.6 - - - +
448C GLU* 1.3 60.9 + - - +
449C THR 3.8 5.6 - - - +
452C GLY* 4.7 8.3 - - - +
453C ALA* 3.6 39.0 - - + +
456C LEU* 3.8 29.2 - - + -
495C VAL* 3.9 6.5 - - + -
496C ALA 3.0 15.7 + - - +
497C THR* 3.3 3.9 - - - -
498C ALA* 3.0 26.3 + - - +
515C PHE* 3.8 16.8 - - + -
516C ASP* 3.4 12.8 - - - +
527C ARG* 4.4 2.6 + - - -
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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