Contacts of the strand formed by residues 427 - 431 (chain F) in PDB entry 2JG7
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 427 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272F ASN* 2.9 39.9 + - - +
273F ALA 3.8 1.4 + - - -
302F THR* 4.5 4.3 - - - -
419F ASN* 4.7 0.3 - - - +
426F LEU* 1.3 85.3 + - - +
428F SER* 1.3 67.7 + - - +
449F CYS* 3.7 7.6 - - - -
451F ILE* 3.6 20.9 - - - +
453F ASN* 4.7 0.2 + - - -
458F THR* 2.6 36.6 + - - -
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Residues in contact with SER 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ALA 3.5 7.2 - - - -
419F ASN* 3.5 21.3 - - - -
427F SER* 1.3 80.4 + - - +
429F SER* 1.3 59.9 + - - +
441F TRP* 3.4 14.0 - - - -
447F SER* 2.7 24.5 + - - -
449F CYS* 3.5 4.2 - - - +
451F ILE 2.9 16.8 + - - +
452F VAL* 3.8 1.4 - - - -
453F ASN* 2.8 32.2 + - - +
458F THR* 4.0 2.2 - - - -
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Residues in contact with SER 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273F ALA 3.0 7.9 + - - +
274F ILE* 3.5 18.3 - - - -
275F ILE* 2.8 26.0 + - - +
428F SER* 1.3 78.4 + - - +
430F ILE* 1.3 67.7 + - - +
431F PHE* 4.3 7.2 - - - -
441F TRP* 3.9 2.3 - - - -
453F ASN* 3.3 8.2 - - - +
456F ILE 2.7 28.1 + - - -
457F PRO 3.0 21.4 + - - -
458F THR* 3.4 0.9 + - - -
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Residues in contact with ILE 430 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275F ILE* 3.3 25.4 - - + +
277F PHE* 4.0 11.4 - - + -
416F PHE* 4.1 1.6 - - + -
429F SER* 1.3 76.2 - - - +
431F PHE* 1.3 63.4 + - - +
432F THR* 3.7 24.8 + - + -
437F ARG* 4.1 19.1 - - + +
438F VAL* 4.4 5.2 - - - -
441F TRP* 3.5 63.7 - - + -
453F ASN 3.1 4.6 + - - -
454F VAL* 3.4 7.5 - - + +
455F ASN* 2.9 24.6 + - - +
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Residues in contact with PHE 431 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274F ILE* 3.7 34.8 - - + -
275F ILE 2.8 11.9 + - - +
276F VAL* 4.4 2.9 - - + -
277F PHE* 3.1 25.3 + - - +
280F ALA* 3.3 11.3 - - + +
281F ASP 6.0 0.4 - - - -
284F LEU* 3.7 21.1 - - + -
285F VAL* 3.7 34.1 - - + -
288F SER* 3.7 26.0 - - - -
429F SER* 4.3 5.4 - - - -
430F ILE* 1.3 77.4 - - - +
432F THR* 1.3 61.7 + - - +
455F ASN* 3.3 40.8 - - - +
456F ILE 3.8 20.6 - - - -
457F PRO* 3.9 1.6 - - + -
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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
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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