Contacts of the strand formed by residues 512 - 519 (chain C) in PDB entry 5UHF
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 ILE 512 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C LEU* 4.8 2.9 - - + -
373C PHE* 3.7 35.6 + - + +
376C ARG 5.7 1.1 + - - +
378C LEU* 4.1 24.7 - - + -
455C LEU* 4.0 13.2 - - + -
482C ARG* 2.9 53.9 + - + +
500C LEU* 3.9 24.0 - - + -
504C ALA* 3.9 12.6 - - + -
505C ARG 3.6 10.5 - - - +
506C VAL* 5.6 1.8 - - + -
511C PHE* 1.3 79.5 - - - +
513C GLU* 1.3 64.7 + - - +
531C LEU 4.0 0.9 - - - +
532C THR* 4.2 5.1 - - - -
533C ALA* 4.5 0.9 + - - +
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Residues in contact with GLU 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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504C ALA* 3.3 8.5 - - - +
505C ARG* 2.9 59.2 + - + +
507C ASN* 3.6 26.9 + - + +
511C PHE 3.9 0.8 + - - -
512C ILE* 1.3 76.4 - - - +
514C THR* 1.3 62.4 + - - +
530C TYR* 3.3 37.1 - - + +
531C LEU 3.2 10.1 - - - +
532C THR* 3.8 28.8 - - + +
535C GLU* 5.1 0.7 - - - +
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Residues in contact with THR 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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480C TYR 4.4 2.7 - - - +
481C GLY 3.3 23.0 + - - +
482C ARG* 3.7 28.9 - - + +
503C TYR* 5.0 0.2 - - - +
513C GLU* 1.3 75.8 - - - +
515C PRO* 1.3 72.8 - - - +
516C TYR* 3.6 30.9 + - + +
530C TYR* 3.6 4.3 - - - -
531C LEU 3.1 20.2 + - - +
585C GLN* 2.6 29.6 + - - +
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Residues in contact with PRO 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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48C LEU* 4.4 9.4 - - + -
503C TYR* 3.1 42.6 - - + +
514C THR* 1.3 92.1 - - - +
516C TYR* 1.3 60.4 - - - +
528C ILE* 3.8 14.6 - - + -
529C VAL 3.9 4.3 - - - +
530C TYR* 3.4 25.3 - - + -
581C VAL* 3.2 26.2 - - + +
585C GLN* 3.2 21.8 + - - -
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Residues in contact with TYR 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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480C TYR* 4.1 7.4 - + - -
482C ARG* 4.2 0.5 + - - -
514C THR* 3.6 35.3 + - + +
515C PRO* 1.3 75.0 - - - +
517C ARG* 1.3 62.1 + - - +
518C LYS 3.8 0.2 + - - -
528C ILE* 3.5 17.0 - - - +
529C VAL* 3.3 20.2 + - - +
531C LEU* 3.7 36.6 - - + -
536C GLU* 2.5 31.5 + - + -
541C VAL* 3.6 14.4 - - + -
562C ARG* 2.7 18.1 + - - -
578C TYR* 4.0 16.4 - - + -
579C MET 3.5 15.9 - - - +
580C ASP* 3.2 23.1 - - - -
581C VAL* 4.3 2.5 - - - -
585C GLN* 4.2 9.9 - - - -
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Residues in contact with ARG 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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43C LYS* 4.5 11.7 - - - +
46C GLU* 5.9 4.0 - - - +
47C PRO* 4.4 36.0 - - + +
516C TYR* 1.3 73.0 - - - +
518C LYS* 1.3 61.0 + - - +
524C VAL* 3.7 14.3 - - + +
525C SER 3.6 19.7 - - - +
526C ASP* 5.0 9.8 + - - +
527C GLU 4.2 3.1 - - - -
528C ILE* 4.9 11.4 - - + +
544C ALA* 4.6 0.6 + - - +
548C ILE* 3.7 13.9 - - - +
578C TYR* 3.3 9.8 - - - +
579C MET* 2.9 76.2 + - + +
580C ASP 4.1 9.3 + - - +
581C VAL* 4.5 12.1 + - + +
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Residues in contact with LYS 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 TYR 3.8 0.6 + - - +
517C ARG* 1.3 73.9 - - - +
519C VAL* 1.3 66.3 + - - +
520C VAL* 5.0 5.8 - - + +
524C VAL* 3.6 0.9 - - - -
525C SER* 2.6 44.7 + - - -
527C GLU* 3.1 54.1 + - + +
529C VAL* 5.2 6.5 - - + -
578C TYR* 3.5 35.2 + - + -
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Residues in contact with VAL 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 ARG 4.7 0.4 - - - +
518C LYS* 1.3 83.8 - - - +
520C VAL* 1.3 64.6 + - - +
521C ASP 4.2 0.2 - - - +
522C GLY* 3.4 31.0 - - - +
523C VAL 3.4 11.0 - - - +
524C VAL* 3.8 26.2 - - + -
554C PHE* 4.9 2.5 - - + -
576C VAL* 3.5 33.4 - - + +
577C ASP* 3.1 26.2 + - - +
578C TYR* 4.5 10.3 - - - -
579C MET* 4.6 5.2 - - + +
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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