Contacts of the strand formed by residues 513 - 520 (chain C) in PDB entry 1U0O
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 513 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509C CYS* 5.2 5.2 - - - -
511C LYS* 3.6 1.9 - - + -
512C LEU* 1.3 75.5 - - - +
514C ASP* 1.3 84.3 + - - +
515C LEU* 3.7 21.5 - - + -
544C LEU* 4.8 7.2 - - + -
550C ARG 3.3 6.5 + - - -
551C ILE* 4.1 13.2 - - + -
552C ARG 2.9 18.5 + - - -
611C ARG* 2.6 24.0 + - - -
615C SER* 3.8 10.8 - - - +
617C ILE* 3.8 28.0 - - + +
694C LEU* 3.5 39.0 - - + +
698C ALA* 4.3 11.0 - - + -
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Residues in contact with ASP 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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513C LEU* 1.3 70.9 - - - +
515C LEU* 1.3 57.2 + - - +
516C VAL 3.9 0.2 + - - -
552C ARG* 3.5 24.8 + - - +
568C LEU* 4.0 12.9 - - + +
606C PHE* 3.6 20.5 - - + -
610C ASP* 5.3 0.9 - - - +
611C ARG* 3.2 29.5 + - - +
614C ALA* 5.2 0.2 - - - -
615C SER 2.9 15.8 + - - +
616C HIS* 2.7 32.6 + - - +
617C ILE 2.7 34.1 + - - +
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Residues in contact with LEU 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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513C LEU* 3.6 12.5 - - + -
514C ASP* 1.3 73.8 - - - +
516C VAL* 1.3 59.9 + - - +
517C PHE* 3.4 35.2 - - + -
540C MET* 4.3 1.1 - - + -
544C LEU* 3.6 27.8 - - + -
551C ILE* 4.6 1.6 - - + -
552C ARG 2.8 10.2 + - - +
553C VAL* 3.0 37.8 - - + +
554C ALA 3.0 3.6 + - - -
568C LEU* 3.9 0.8 - - - +
617C ILE* 3.3 24.7 - - + +
619C LEU* 4.5 10.8 - - + -
694C LEU* 3.5 35.0 - - + -
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Residues in contact with VAL 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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515C LEU* 1.3 78.0 - - - +
517C PHE* 1.3 62.3 + - - +
518C LEU* 3.7 25.0 + - + -
554C ALA* 3.6 14.1 - - + +
556C VAL* 4.9 1.1 - - + -
568C LEU* 4.5 2.5 - - + -
605C ILE* 3.6 49.6 - - + -
606C PHE* 3.9 18.8 - - + -
617C ILE 2.6 12.3 + - - +
618C THR* 3.3 11.9 - - + +
619C LEU* 2.7 32.4 + - - +
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Residues in contact with PHE 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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515C LEU* 3.4 27.1 - - + -
516C VAL* 1.3 72.7 - - - +
518C LEU* 1.3 63.0 + - - +
519C LEU* 3.8 15.3 - - + +
536C PHE* 5.4 0.9 - + - -
537C VAL* 4.1 27.6 - - + -
540C MET* 3.4 37.5 - - + -
541C MET* 4.3 9.6 - - + -
544C LEU* 4.1 9.9 - - + -
553C VAL* 3.0 40.8 - - + -
554C ALA 3.0 9.0 + - - +
555C VAL* 3.6 12.0 - - + -
556C VAL 3.1 25.8 + - - +
619C LEU* 3.7 17.7 - - + -
621C LEU* 4.4 3.4 - - + -
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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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516C VAL* 3.7 12.1 - - + -
517C PHE* 1.3 77.1 - - - +
519C LEU* 1.3 61.9 + - - +
520C ASP 3.8 0.2 + - - -
556C VAL* 3.6 20.6 - - + -
558C TYR* 3.7 6.0 - - + -
597C VAL* 3.6 37.0 - - + +
598C LEU* 4.2 10.1 - - + -
600C TYR* 5.7 0.2 - - + -
601C THR* 3.5 16.4 - - - +
618C THR* 3.4 31.6 - - + -
619C LEU 3.0 8.1 + - - -
620C LEU* 3.7 20.1 - - + -
621C LEU* 2.8 34.2 + - - +
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Residues in contact with LEU 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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517C PHE* 3.8 28.5 - - + +
518C LEU* 1.3 73.4 - - - +
520C ASP* 1.3 54.3 + - - +
521C GLY* 2.6 17.3 + - - -
530C PHE* 4.6 14.6 - - + -
533C LEU* 3.5 27.1 - - + -
534C LYS* 4.8 8.5 - - + -
537C VAL* 3.9 24.0 - - + -
555C VAL* 4.0 7.9 - - + -
556C VAL 2.9 14.7 + - - +
557C GLU* 3.8 5.0 - - - -
558C TYR* 3.0 23.5 + - - -
584C ILE* 4.2 25.1 - - + -
621C LEU* 3.8 6.1 - - + -
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Residues in contact with ASP 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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519C LEU* 1.3 65.8 - - - +
521C GLY* 1.3 57.3 + - - +
522C SER* 2.7 30.5 + - - -
525C LEU* 3.4 22.5 - - + +
533C LEU* 4.3 5.4 - - + +
558C TYR* 3.3 16.6 + - - +
592C ALA* 3.2 10.3 - - - +
621C LEU 2.8 18.4 + - - +
622C THR* 2.9 11.1 + - - -
623C ALA* 2.5 40.5 + - + +
624C SER* 2.8 19.3 + - - -
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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