Contacts of the helix formed by residues 503 - 518 (chain C) in PDB entry 1UER
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 503 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497C ILE* 4.3 3.5 - - - +
498C ASP* 3.5 15.5 + - - +
501C PHE* 3.3 4.6 + - - +
502C GLY* 1.3 78.6 - - - +
504C PHE* 1.3 58.7 + - - +
505C GLU* 3.7 7.3 + - - +
506C LYS* 3.1 22.5 + - - +
507C PHE* 3.0 28.1 + - - +
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Residues in contact with PHE 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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487C GLY 3.5 23.8 - - - -
488C ALA* 3.7 18.6 - - + -
489C PRO* 3.4 27.1 - - + -
497C ILE* 4.2 11.4 - - + -
498C ASP* 3.7 8.4 + - - +
503C SER* 1.3 73.4 - - - +
505C GLU* 1.3 64.0 + - + +
507C PHE* 3.2 13.6 + + - +
508C LYS* 2.9 70.8 + - + +
579C TRP* 4.3 3.8 - + + -
584C TRP* 3.4 31.0 - + - -
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Residues in contact with GLU 505 (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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503C SER* 3.3 7.2 + - - +
504C PHE* 1.3 83.4 - - + +
506C LYS* 1.3 61.2 + - - +
508C LYS* 3.0 35.9 + - - +
509C GLU* 3.1 21.8 + - - +
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Residues in contact with LYS 506 (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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501C PHE 3.1 25.1 - - - +
502C GLY* 4.9 0.9 - - - -
503C SER* 3.1 19.2 + - - +
505C GLU* 1.3 76.1 - - - +
507C PHE* 1.3 64.3 + - - +
509C GLU* 3.2 26.1 + - - +
510C GLU* 2.4 66.6 + - - +
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Residues in contact with PHE 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497C ILE* 3.7 19.7 - - + -
501C PHE* 3.8 36.7 - + + +
503C SER 3.0 13.8 + - - +
504C PHE* 3.4 23.6 - + - +
506C LYS* 1.3 77.5 - - - +
508C LYS* 1.3 58.2 + - - +
510C GLU* 3.1 3.7 + - - +
511C PHE* 2.9 60.3 + + - +
526C LEU* 3.8 36.3 - - + -
536C ILE* 4.1 6.1 - - + -
554C LEU* 4.8 1.6 - - + -
579C TRP* 3.5 25.6 - + - -
584C TRP* 4.3 11.9 - + - -
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Residues in contact with LYS 508 (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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504C PHE* 2.9 47.4 + - + +
505C GLU* 3.0 41.5 + - - +
506C LYS 3.3 0.2 - - - -
507C PHE* 1.3 77.2 - - + +
509C GLU* 1.3 58.3 + - - +
511C PHE* 3.2 0.9 + - - +
512C ASN* 2.8 40.0 + - - +
579C TRP* 3.4 62.4 - - + +
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Residues in contact with GLU 509 (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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505C GLU 3.1 13.8 + - - +
506C LYS* 3.2 31.4 + - - +
508C LYS* 1.3 76.7 - - - +
510C GLU* 1.3 66.6 + - - +
512C ASN* 3.8 9.2 - - - +
513C THR* 3.0 44.4 + - - +
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Residues in contact with GLU 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501C PHE* 3.5 28.6 - - - +
506C LYS* 2.4 56.0 + - - +
507C PHE* 3.6 6.3 - - - +
509C GLU* 1.3 79.1 - - - +
511C PHE* 1.3 60.2 + - - +
513C THR* 3.4 5.5 + - - -
514C ALA* 3.0 28.6 + - - +
536C ILE* 4.1 13.9 - - + +
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Residues in contact with PHE 511 (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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507C PHE* 2.9 33.2 + + + +
508C LYS 3.5 4.0 - - - +
510C GLU* 1.3 75.1 - - - +
512C ASN* 1.3 66.1 + - - +
514C ALA* 3.2 5.4 + - - +
515C GLY* 3.0 18.9 + - - -
524C VAL* 3.5 38.5 - - + +
525C TRP 3.7 3.1 - - - -
526C LEU* 3.5 36.1 - - + -
536C ILE* 3.9 13.9 - - + +
554C LEU* 3.8 15.9 - - + -
556C PHE* 3.5 35.4 - + - -
575C LEU* 5.2 0.3 - - - +
579C TRP* 3.6 27.1 - + + -
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Residues in contact with ASN 512 (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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508C LYS* 2.8 29.5 + - - +
509C GLU* 3.8 7.7 - - - +
511C PHE* 1.3 73.4 - - - +
513C THR* 1.3 57.4 + - - +
515C GLY* 3.2 2.4 + - - -
516C THR* 2.9 38.5 + - + +
556C PHE* 4.6 1.6 - - - -
572C ALA 5.8 0.2 - - - +
575C LEU* 3.7 27.5 - - + +
576C LYS* 4.5 22.6 - - - +
579C TRP* 2.8 34.2 + - - +
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Residues in contact with THR 513 (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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509C GLU* 3.0 30.8 + - - +
510C GLU* 3.6 7.4 - - - -
511C PHE 3.2 0.2 - - - -
512C ASN* 1.3 78.4 - - - +
514C ALA* 1.3 57.4 + - - +
516C THR* 3.2 7.1 + - - +
517C THR* 2.9 51.3 + - + +
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Residues in contact with ALA 514 (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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510C GLU 3.0 13.5 + - - +
511C PHE 3.5 8.7 - - - +
513C THR* 1.3 77.5 - - - +
515C GLY* 1.3 62.6 + - - +
517C THR* 3.8 5.6 - - - -
518C LEU* 3.2 10.0 + - - +
524C VAL* 3.9 17.9 - - + -
536C ILE* 3.9 15.3 - - + -
538C LYS* 3.0 38.4 + - + +
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Residues in contact with GLY 515 (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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511C PHE 3.0 12.9 + - - -
512C ASN 3.2 2.9 + - - -
514C ALA* 1.3 79.6 - - - +
516C THR* 1.3 57.5 + - - +
517C THR 3.5 0.5 + - - -
518C LEU* 3.5 8.0 + - - +
524C VAL* 4.3 17.9 - - - +
558C VAL* 4.0 6.7 - - - +
571C ARG* 2.9 26.9 + - - -
575C LEU* 3.7 17.3 - - - -
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Residues in contact with THR 516 (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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512C ASN* 2.9 20.8 + - + +
513C THR* 3.2 13.9 + - - +
515C GLY* 1.3 77.0 - - - +
517C THR* 1.3 67.5 + - - +
518C LEU 3.4 0.9 + - - +
571C ARG* 4.1 15.8 + - - +
572C ALA* 3.8 31.0 - - + +
575C LEU* 3.6 14.8 - - + -
576C LYS* 5.9 0.4 - - - +
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Residues in contact with THR 517 (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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513C THR* 2.9 36.0 + - + +
514C ALA* 3.5 1.0 + - - -
516C THR* 1.3 81.7 - - - +
518C LEU* 1.3 64.3 + - - +
519C PHE* 3.1 8.4 + - - +
538C LYS* 3.4 22.6 + - - -
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Residues in contact with LEU 518 (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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514C ALA 3.2 16.9 + - - +
515C GLY 3.8 7.2 - - - +
516C THR 3.4 2.1 - - - +
517C THR* 1.3 73.5 - - - +
519C PHE* 1.3 73.2 + - - +
520C GLY 3.5 6.7 + - - +
521C SER 3.6 26.5 - - - +
522C GLY* 4.0 1.3 - - - +
523C TRP 3.4 39.5 - - - +
524C VAL* 4.6 2.9 - - + +
538C LYS* 3.5 20.6 - - + +
539C GLU 4.0 13.0 - - - +
540C PRO* 4.9 5.6 - - + -
558C VAL* 4.0 7.6 - - + -
571C ARG* 2.8 27.6 + - - +
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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