Contacts of the helix formed by residues 515 - 528 (chain C) in PDB entry 5HP1
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 515 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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360C ALA 4.7 0.2 + - - -
361C HIS* 4.1 8.1 - - - -
479C LEU* 5.2 1.9 - - - +
513C SER* 3.1 10.6 + - - -
514C GLU* 1.3 77.1 - - - +
516C GLU* 1.3 64.7 + - - +
517C LEU* 3.5 8.1 + - - +
518C VAL* 3.2 27.1 + - - +
519C ASN* 3.0 24.4 + - - -
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Residues in contact with GLU 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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514C GLU 3.9 3.6 + - - -
515C SER* 1.3 71.2 + - - +
517C LEU* 1.3 57.5 + - - +
519C ASN* 3.2 16.4 + - - +
520C GLN* 2.9 54.0 + - - +
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Residues in contact with LEU 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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476C LYS* 3.9 15.7 - - + +
479C LEU* 3.7 29.4 - - + +
480C GLN* 3.5 27.1 - - - +
483C TYR* 3.9 30.7 - - + -
515C SER* 3.2 6.8 + - - +
516C GLU* 1.3 78.8 - - - +
518C VAL* 1.3 61.9 + - - +
520C GLN* 2.9 17.8 + - - +
521C ILE* 2.9 35.9 + - + +
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Residues in contact with VAL 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361C HIS* 3.7 25.4 - - + +
479C LEU* 3.9 25.6 - - + -
505C ILE* 4.2 19.7 - - + -
506C ILE* 6.4 0.7 - - + -
510C PRO* 4.9 1.3 - - + -
513C SER* 3.6 21.3 - - - +
515C SER* 3.2 20.5 + - - +
517C LEU* 1.3 75.9 - - - +
519C ASN* 1.3 58.5 + - - +
521C ILE* 3.1 11.6 + - + +
522C ILE* 2.9 40.2 + - + +
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Residues in contact with ASN 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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511C ASP 4.9 0.7 - - - +
512C LYS* 3.6 8.0 - - - -
513C SER* 2.6 47.5 + - - -
514C GLU 4.7 0.4 - - - -
515C SER 3.0 18.9 + - - -
516C GLU* 3.4 18.9 + - - +
518C VAL* 1.3 74.9 - - - +
520C GLN* 1.3 62.6 + - - +
522C ILE* 3.4 9.3 + - - +
523C GLU* 3.0 23.2 + - - +
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Residues in contact with GLN 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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483C TYR* 3.3 39.7 + - + +
516C GLU* 2.9 40.6 + - - +
517C LEU* 2.9 25.8 + - - +
519C ASN* 1.3 75.7 - - - +
521C ILE* 1.3 62.5 + - - +
523C GLU* 3.3 12.9 + - - +
524C GLN* 3.1 24.9 + - - +
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Residues in contact with ILE 521 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C LEU* 3.6 42.0 - - + +
482C ILE* 4.9 3.1 - - + -
483C TYR* 3.9 26.9 - - + +
486C LEU* 3.8 16.8 - - + -
506C ILE* 4.5 17.9 - - + -
517C LEU* 2.9 27.8 + - + +
518C VAL* 3.1 12.3 + - + +
520C GLN* 1.3 73.9 - - - +
522C ILE* 1.3 62.2 + - + +
524C GLN* 3.1 8.8 + - - +
525C LEU* 2.8 41.8 + - + +
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Residues in contact with ILE 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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427C TYR* 4.0 10.5 - - + +
510C PRO* 3.4 35.9 - - + +
511C ASP* 4.1 15.3 - - - +
512C LYS 4.0 18.6 - - - +
518C VAL* 2.9 40.5 + - + +
519C ASN* 3.6 13.9 - - - +
521C ILE* 1.3 77.0 - - + +
523C GLU* 1.3 59.1 + - - +
525C LEU* 3.1 12.1 + - + +
526C ILE* 2.9 46.5 + - + +
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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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519C ASN 3.0 13.8 + - - +
520C GLN* 3.6 15.8 - - - +
522C ILE* 1.3 76.2 - - - +
524C GLN* 1.3 70.4 + - - +
526C ILE* 3.4 12.5 + - - +
527C LYS* 2.8 55.7 + - + +
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Residues in contact with GLN 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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483C TYR* 3.5 32.1 + - + -
486C LEU* 3.5 36.4 - - + +
487C GLN* 3.9 19.0 - - - +
520C GLN 3.1 8.3 + - - +
521C ILE 3.1 9.7 + - - +
523C GLU* 1.3 85.6 + - - +
525C LEU* 1.3 65.3 + - - +
527C LYS* 3.1 28.9 + - - +
528C LYS* 3.3 23.1 + - - +
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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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427C TYR* 3.6 49.9 - - + +
429C LEU* 4.5 9.0 - - + -
486C LEU* 4.0 27.1 - - + -
506C ILE* 3.8 22.2 - - + -
521C ILE* 2.8 32.1 + - + +
522C ILE* 3.1 10.1 + - + +
524C GLN* 1.3 71.9 - - - +
526C ILE* 1.3 63.4 + - - +
528C LYS* 3.2 19.3 + - - +
531C VAL* 4.0 25.9 - - + +
533C LEU* 5.8 1.1 - - + -
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Residues in contact with ILE 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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426C TRP* 3.7 58.5 - - + +
427C TYR* 4.0 5.6 - - + -
511C ASP* 5.8 0.9 - - + +
522C ILE* 2.9 40.5 + - + +
523C GLU* 3.7 9.0 - - - +
524C GLN 3.2 0.4 - - - -
525C LEU* 1.3 76.9 - - - +
527C LYS* 1.3 64.7 + - + +
528C LYS 3.3 6.2 + - - +
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Residues in contact with LYS 527 (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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491C LEU* 3.8 16.6 - - - +
523C GLU* 2.8 47.1 + - + +
524C GLN* 3.1 25.3 + - - +
526C ILE* 1.3 78.8 - - + +
528C LYS* 1.3 65.4 + - + +
529C GLU* 5.5 0.2 - - - +
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Residues in contact with LYS 528 (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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486C LEU* 2.8 33.3 + - + +
489C SER* 2.6 37.4 + - - +
490C GLY 2.7 24.3 + - - +
491C LEU* 3.8 10.1 - - + +
493C VAL* 4.4 3.1 - - + -
524C GLN* 3.3 23.3 + - - +
525C LEU* 3.2 9.6 + - - +
526C ILE 3.2 9.5 - - - +
527C LYS* 1.3 84.1 - - - +
529C GLU* 1.3 62.6 + - - +
530C LYS 4.3 0.2 - - - +
531C VAL* 3.5 33.7 - - + -
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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