Contacts of the helix formed by residues 2553 - 2567 (chain C) in PDB entry 5Y3R
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 HIS2553 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2552C VAL* 1.3 109.2 + - + +
2554C PHE* 1.3 63.2 + - - +
2555C LEU* 3.0 6.5 - - - +
2556C SER* 2.1 42.1 + - - +
2557C LEU* 4.1 4.9 - - + -
2803C ILE* 5.8 10.0 - - + +
2852C PRO* 5.6 3.2 - - + +
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Residues in contact with PHE2554 (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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2546C TYR* 5.1 5.1 - + + -
2549C LYS* 3.1 42.8 + - + +
2551C GLU 3.0 26.2 - - - -
2552C VAL* 2.7 25.9 + - + +
2553C HIS* 1.3 78.6 - - - +
2555C LEU* 1.3 100.6 + - + +
2557C LEU* 2.6 46.3 + - + +
2558C ALA* 2.9 8.9 + - + +
2843C PHE* 4.2 27.4 - + - -
2847C THR* 6.2 0.9 - - + -
2852C PRO* 5.2 1.6 - - + -
2853C PRO* 4.5 14.8 - - + -
2856C SER* 4.9 1.1 - - - -
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Residues in contact with LEU2555 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2546C TYR* 6.5 0.9 - - + -
2553C HIS* 2.9 3.8 + - - +
2554C PHE* 1.3 114.8 - - + +
2556C SER* 1.3 65.0 + - - +
2557C LEU 2.8 1.0 + - - -
2558C ALA* 3.0 7.7 + - + +
2559C THR* 2.9 29.1 + - + +
2808C LEU* 4.1 16.2 - - + -
2809C PHE* 5.1 7.6 - - + -
2812C LEU* 6.4 2.2 - - + -
2843C PHE* 6.1 0.4 - - + -
2852C PRO* 4.6 17.0 - - + +
2855C VAL* 6.2 0.2 - - + -
2856C SER* 4.3 13.5 - - - +
2859C GLN* 4.2 22.7 - - - +
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Residues in contact with SER2556 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2553C HIS* 2.1 31.3 + - - +
2555C LEU* 1.3 74.7 - - - +
2557C LEU* 1.3 76.4 + - - +
2559C THR* 2.0 28.1 + - - -
2560C ASN* 2.5 20.4 + - - +
2799C GLN 5.3 3.1 - - - -
2800C ARG* 3.7 24.2 - - - -
2802C PRO 5.7 2.9 - - - -
2808C LEU* 4.7 5.6 - - - +
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Residues in contact with LEU2557 (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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2510C LEU* 5.3 12.1 - - + +
2511C ILE* 5.9 6.3 - - + -
2512C ASP* 5.6 3.1 - - - +
2519C LEU* 4.3 14.1 - - + -
2552C VAL 4.9 2.2 - - - +
2553C HIS* 3.9 4.3 - - + +
2554C PHE* 2.6 38.1 + - + +
2556C SER* 1.3 87.5 - - - +
2558C ALA* 1.3 63.2 + - - +
2560C ASN* 3.7 2.8 - - + +
2561C PHE* 2.9 49.0 + - + -
2800C ARG* 4.2 23.6 - - - +
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Residues in contact with ALA2558 (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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2542C LEU* 4.0 10.9 - - + +
2546C TYR* 3.3 36.9 - - + +
2554C PHE* 2.9 12.5 + - + +
2555C LEU* 3.7 9.9 - - + +
2557C LEU* 1.3 71.2 - - - +
2559C THR* 1.3 68.5 + - + +
2561C PHE* 3.0 18.2 - - - +
2562C LEU* 3.0 21.1 + - - +
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Residues in contact with THR2559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2555C LEU* 2.9 16.3 + - + +
2556C SER* 2.0 36.6 + - - -
2558C ALA* 1.3 72.4 - - + +
2560C ASN* 1.3 58.8 + - - -
2562C LEU* 2.4 34.4 + - - +
2563C LEU* 2.8 23.3 + - - +
2799C GLN 5.7 0.3 + - - -
2808C LEU* 3.6 45.0 - - + +
2811C SER* 5.3 2.5 - - - +
2812C LEU* 6.1 2.7 - - + -
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Residues in contact with ASN2560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2556C SER* 2.5 26.9 + - - +
2557C LEU* 3.8 3.5 - - + +
2559C THR* 1.3 83.5 + - - +
2561C PHE* 1.3 68.8 + - + +
2563C LEU* 2.8 32.0 + - - +
2564C GLU* 2.9 13.0 + - - +
2796C ALA* 3.7 10.7 + - + +
2799C GLN 4.5 1.6 + - - -
2800C ARG* 3.0 59.5 + - + +
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Residues in contact with PHE2561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2510C LEU* 4.1 24.0 - - + -
2519C LEU* 4.4 8.3 - - + -
2523C ASN* 3.3 41.1 - - - -
2527C HIS* 5.7 5.2 - + + +
2531C LEU* 6.0 7.6 - - + -
2542C LEU* 4.9 4.9 - - + -
2546C TYR* 4.1 12.3 - + - -
2557C LEU* 2.9 47.8 + - + -
2558C ALA* 3.0 17.7 - - - +
2560C ASN* 1.3 81.4 - - + +
2562C LEU* 1.3 67.5 + - + +
2563C LEU 2.8 3.1 + - - -
2564C GLU* 2.9 20.7 + - - +
2565C MET* 2.9 10.8 + - - +
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Residues in contact with LEU2562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2535C THR* 4.4 11.2 - - + +
2538C ARG* 3.4 32.3 - - + -
2539C LEU* 3.7 29.8 - - + +
2542C LEU* 3.5 36.1 - - + -
2558C ALA 3.7 6.1 - - - +
2559C THR* 2.4 19.1 + - - +
2561C PHE* 1.3 78.8 - - + +
2563C LEU* 1.3 61.5 + - + +
2565C MET* 3.5 20.0 - - + -
2566C THR* 2.8 31.5 + - - +
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Residues in contact with LEU2563 (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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898C PHE* 5.0 5.9 - - + -
2559C THR* 2.8 19.0 + - - +
2560C ASN* 2.8 39.2 + - - +
2561C PHE 2.8 0.2 + - - -
2562C LEU* 1.3 81.8 - - + +
2564C GLU* 1.3 66.1 + - - +
2566C THR* 3.3 24.2 - - + +
2567C SER* 3.6 10.0 + - - +
2792C THR* 5.1 4.8 - - + +
2795C GLN* 5.9 2.9 - - - +
2796C ALA* 3.7 29.8 - - + -
2799C GLN* 5.0 7.4 - - + +
2808C LEU* 6.1 2.2 - - + -
2811C SER* 5.9 7.0 - - - -
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Residues in contact with GLU2564 (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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2524C PHE* 3.4 29.5 - - - -
2527C HIS* 3.9 20.9 + - - -
2560C ASN 2.9 9.0 + - - +
2561C PHE* 2.9 12.5 + - - +
2563C LEU* 1.3 76.8 - - - +
2565C MET* 1.3 56.7 + - - +
2567C SER 2.6 25.7 - - - +
2568C MET* 3.3 8.9 + - + +
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Residues in contact with MET2565 (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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900C GLU* 5.4 1.3 - - - +
2533C SER* 4.1 5.8 - - - -
2534C ASN* 3.2 42.6 - - - +
2535C THR* 4.0 15.2 + - - +
2538C ARG* 2.7 29.4 - - - +
2561C PHE 2.9 7.7 + - - +
2562C LEU* 3.5 25.8 - - + -
2564C GLU* 1.3 79.1 - - - +
2566C THR* 1.3 66.7 + - - +
2567C SER 3.0 1.2 + - - -
2568C MET* 3.3 36.2 + - + +
2570C PRO* 5.6 0.2 - - - +
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Residues in contact with THR2566 (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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898C PHE* 2.9 70.7 - - + +
900C GLU* 5.4 4.3 + - - +
901C MET* 4.9 9.6 - - - +
903C PRO* 4.8 3.3 - - - +
2535C THR* 4.8 14.4 - - - +
2562C LEU* 2.8 26.0 + - - +
2563C LEU* 3.3 20.4 - - + +
2565C MET* 1.3 77.3 - - - +
2567C SER* 1.3 60.3 + - - +
2570C PRO* 4.2 3.3 - - - +
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Residues in contact with SER2567 (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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897C PRO 3.7 2.5 - - - -
898C PHE* 3.2 29.6 - - - -
2563C LEU 3.6 3.5 + - - +
2564C GLU* 2.6 19.7 - - - +
2566C THR* 1.3 77.9 - - - +
2568C MET* 1.3 63.8 + - - +
2570C PRO* 3.4 13.5 - - - -
2571C ASP* 3.7 23.5 - - - +
2792C THR* 3.5 14.4 - - - +
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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