Contacts of the strand formed by residues 498 - 504 (chain C) in PDB entry 1P4K
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 GLY 498 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464C LEU* 3.6 15.0 - - - +
493C VAL* 3.8 0.2 - - - -
494C ASP* 2.9 31.4 + - - +
497C ILE* 1.3 79.3 - - - +
499C ALA* 1.3 61.0 + - - -
519C VAL* 4.0 6.7 - - - +
522C MET* 4.0 9.6 - - - -
560C LEU 3.0 14.4 - - - -
561C ASN* 3.8 0.9 - - - -
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Residues in contact with ALA 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C ILE* 3.6 21.8 - - + +
464C LEU* 4.4 12.7 - - + +
465C SER 5.1 1.3 - - - +
492C PHE 3.3 12.6 - - - +
493C VAL* 3.7 23.8 - - + -
498C GLY* 1.3 74.4 - - - +
500C ALA* 1.3 63.6 + - - +
519C VAL* 4.0 3.4 - - - -
522C MET* 3.7 1.7 - - - +
559C ALA* 3.3 4.2 - - - +
560C LEU* 2.8 31.9 + - + +
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Residues in contact with ALA 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456C ILE* 4.1 4.7 - - - +
491C LEU* 3.5 2.6 - - - +
492C PHE 2.9 30.9 + - - +
499C ALA* 1.3 78.1 - - - +
501C THR* 1.3 63.1 + - - +
515C THR* 3.3 12.2 - - + +
518C VAL* 3.6 36.6 - - + -
519C VAL* 4.0 8.5 - - + +
557C PHE* 5.6 0.7 - - + -
558C ILE 3.3 13.9 - - - +
559C ALA* 4.1 0.4 - - + -
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Residues in contact with THR 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C THR* 4.3 3.4 - - + +
454C GLY* 3.4 35.6 - - - -
455C MET 3.9 2.2 - - - +
456C ILE* 4.0 7.9 - - + -
468C CYS* 4.0 4.9 - - - +
490C GLY 2.9 18.5 + - - -
491C LEU* 3.9 14.6 - - - +
500C ALA* 1.3 75.2 - - - +
502C ALA* 1.3 61.6 + - - +
515C THR* 3.5 4.0 - - - -
556C GLY 4.1 0.2 - - - +
557C PHE* 3.6 3.8 - - - -
558C ILE* 3.1 57.2 + - + +
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Residues in contact with ALA 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C THR* 5.0 3.1 - - - +
452C THR* 4.2 2.1 + - - -
454C GLY* 5.0 0.9 - - - -
468C CYS* 4.1 12.3 - - - -
483C ASP* 3.7 22.4 - - - +
484C SER* 5.2 0.7 + - - -
489C ALA 4.2 0.9 - - - +
490C GLY 3.0 8.8 + - - +
501C THR* 1.3 81.1 + - - +
503C THR* 1.3 64.5 + - - +
509C VAL* 3.9 12.8 - - + -
515C THR* 3.7 4.9 - - + +
556C GLY 3.4 7.6 - - - +
557C PHE* 3.6 29.6 - - + -
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Residues in contact with THR 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310C THR* 4.0 14.6 - - + -
311C TRP* 2.8 36.1 + - + +
450C HIS 4.8 0.7 + - - -
452C THR* 2.6 29.0 + - - +
454C GLY 5.7 0.2 - - - -
483C ASP* 4.9 6.1 - - - -
502C ALA* 1.3 76.9 - - - +
504C GLY* 1.3 60.5 + - - +
509C VAL* 5.3 1.8 - - - -
555C VAL* 3.3 7.1 - - - +
556C GLY 2.9 37.4 + - - +
575C PHE* 3.6 23.3 - - + -
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Residues in contact with GLY 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2C GOL 4.7 2.4 + - - -
4C GOL 3.2 15.1 - - - -
311C TRP* 5.2 0.4 - - - -
445C VAL* 3.9 24.5 - - - -
450C HIS* 3.3 11.1 + - - -
452C THR* 4.7 1.0 + - - -
483C ASP* 5.3 0.2 + - - -
503C THR* 1.3 81.4 + - - +
505C HIS* 1.3 60.3 + - - -
506C GLY* 2.8 10.1 + - - -
509C VAL* 5.7 0.2 - - - -
554C GLN* 3.2 12.3 - - - -
555C VAL* 4.3 0.7 - - - -
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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