Contacts of the helix formed by residues 514 - 526 (chain C) in PDB entry 2O1S
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 LEU 514 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510C ASN* 3.7 3.8 - - - +
511C PHE 5.3 0.9 + - - +
512C GLY 3.3 2.4 + - - -
513C THR* 1.3 77.1 + - - +
515C MSE 1.3 64.4 + - - +
516C PRO* 3.3 2.2 - - - -
517C GLU* 2.9 23.6 + - + +
518C ALA* 2.9 10.2 + - - +
556C VAL* 3.8 29.4 - - + -
557C GLU* 3.9 23.6 - - - +
558C GLU* 4.0 33.9 - - + +
601C ARG* 4.3 18.8 - - + +
606C LEU* 4.1 28.0 - - + +
611C MSE 4.2 11.9 - - + -
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Residues in contact with MSE 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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452C SER* 3.4 25.1 - - - +
500C LYS* 4.5 12.1 - - + -
510C ASN* 3.3 25.6 - - + +
512C GLY 3.6 7.6 - - - +
513C THR 3.0 1.8 - - - -
514C LEU* 1.3 76.6 - - - +
516C PRO* 1.3 72.3 - - + +
518C ALA* 3.0 1.5 + - - -
519C ALA* 2.7 27.3 + - + +
529C LEU* 4.0 28.7 - - + -
530C VAL 4.1 4.0 - - - +
531C ASP* 3.4 47.3 - - + +
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Residues in contact with PRO 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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452C SER 5.1 3.4 - - - +
482C VAL* 4.5 21.1 - - + -
513C THR* 3.2 17.3 - - - +
514C LEU 3.4 1.8 - - - -
515C MSE 1.3 95.8 - - + +
517C GLU* 1.3 67.9 + - + +
519C ALA* 3.7 6.5 + - + +
520C LYS* 3.3 25.3 + - - +
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Residues in contact with GLU 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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514C LEU* 2.9 16.1 + - + +
516C PRO* 1.3 83.0 - - + +
518C ALA* 1.3 66.7 + - - +
519C ALA 3.1 1.6 - - - -
520C LYS* 3.0 31.1 + - - +
521C VAL* 3.1 18.1 + - - +
606C LEU 4.1 11.4 - - - +
607C ASP* 3.5 18.6 - - + +
608C ALA* 2.6 39.5 + - - +
611C MSE 4.4 4.9 - - - -
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Residues in contact with ALA 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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508C ILE* 4.0 19.6 - - + +
510C ASN* 3.9 27.6 - - + +
514C LEU 2.9 12.7 + - - +
515C MSE 3.5 10.3 - - - +
517C GLU* 1.3 74.9 - - - +
519C ALA* 1.3 58.4 + - - +
521C VAL* 3.2 7.6 + - - +
522C ALA* 2.9 26.3 + - - +
529C LEU* 4.2 2.7 - - + -
556C VAL* 4.5 8.7 - - + -
611C MSE 4.3 10.4 - - - -
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Residues in contact with ALA 519 (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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515C MSE 2.7 24.4 + - + +
516C PRO* 3.7 7.2 - - + +
518C ALA* 1.3 70.7 - - - +
520C LYS* 1.3 66.8 + - + +
522C ALA* 2.9 4.0 + - - +
523C GLU* 2.9 28.2 + - + +
529C LEU* 4.0 25.9 - - + +
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Residues in contact with LYS 520 (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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516C PRO 3.3 13.0 + - - +
517C GLU* 3.0 33.2 + - - +
519C ALA* 1.3 77.7 - - + +
521C VAL* 1.3 57.3 + - - +
523C GLU* 3.3 7.2 + - - +
524C SER* 2.9 29.9 + - - -
608C ALA* 3.7 18.0 - - + +
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Residues in contact with VAL 521 (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 ILE* 3.9 10.3 - - + -
517C GLU 3.1 14.5 + - - +
518C ALA* 3.4 7.6 - - - +
519C ALA 3.1 0.2 - - - -
520C LYS* 1.3 77.0 - - - +
522C ALA* 1.3 62.0 + - - +
524C SER* 3.4 5.2 + - - -
525C LEU* 3.0 34.0 + - + +
608C ALA* 3.6 32.8 - - + +
611C MSE 3.7 19.1 - - + -
612C GLU* 4.5 10.1 - - + +
615C ILE* 3.9 28.5 - - + -
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Residues in contact with ALA 522 (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 ARG* 4.0 7.6 - - - -
508C ILE* 3.8 12.8 - - + -
518C ALA 2.9 12.6 + - - +
519C ALA* 2.9 10.4 + - - +
521C VAL* 1.3 78.5 - - - +
523C GLU* 1.3 52.6 + - - +
526C ASN* 2.7 31.7 + - - -
527C ALA* 2.9 27.1 + - - +
529C LEU* 4.0 26.9 - - + -
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Residues in contact with GLU 523 (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 ARG* 2.5 47.9 + - - +
519C ALA* 2.9 16.2 + - + +
520C LYS* 3.6 10.3 - - - +
522C ALA* 1.3 77.0 - - - +
524C SER* 1.3 63.2 + - - +
526C ASN* 3.3 11.1 + - - +
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Residues in contact with SER 524 (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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520C LYS 2.9 17.5 + - - -
521C VAL* 3.7 5.2 - - - -
523C GLU* 1.3 78.8 - - - +
525C LEU* 1.3 60.1 + - - +
526C ASN* 5.3 0.2 - - - +
612C GLU* 2.8 35.5 + - - -
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Residues in contact with LEU 525 (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 GLU 4.9 2.3 - - - +
505C LYS* 5.0 12.8 + - - +
506C LEU* 4.3 12.1 - - + +
508C ILE* 5.5 1.8 - - + -
521C VAL* 3.0 24.0 + - + +
522C ALA 4.5 0.7 - - - +
524C SER* 1.3 79.1 - - - +
526C ASN* 1.3 73.5 + - - +
527C ALA* 4.4 8.6 - - + +
612C GLU* 3.9 29.2 - - + +
615C ILE* 3.8 41.5 - - + -
616C LYS* 3.9 21.5 - - - +
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Residues in contact with ASN 526 (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 ARG* 2.6 34.6 + - - +
502C ARG 5.1 0.5 - - - +
503C GLY* 4.7 3.0 - - - -
504C GLU* 2.8 46.8 + - - +
522C ALA 2.7 11.1 + - - -
523C GLU 3.3 7.5 + - - +
524C SER 5.3 0.4 - - - +
525C LEU* 1.3 78.4 - - - +
527C ALA* 1.3 55.7 + - - +
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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