Contacts of the helix formed by residues 2885 - 2896 (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 GLN2885 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2854C PHE* 3.3 44.8 - - + +
2855C VAL* 4.9 2.6 - - - +
2857C CYS* 5.0 6.5 - - + -
2858C ILE* 3.7 21.7 - - + +
2877C SER* 4.8 7.1 + - - +
2882C ALA* 2.5 29.4 + - + +
2883C SER* 2.9 9.5 - - - -
2884C LEU* 1.3 77.0 + - - +
2886C GLN* 1.3 62.8 + - - +
2887C PRO 3.5 0.2 - - - -
2888C VAL* 2.9 36.7 + - + +
2889C GLY 3.9 0.5 + - - -
3116C SER 5.5 1.0 + - - -
3895C GLU* 2.7 17.9 + - - -
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Residues in contact with GLN2886 (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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2877C SER* 5.5 6.4 + - - -
2882C ALA* 4.8 9.1 - - + +
2883C SER 3.1 17.7 + - - +
2884C LEU* 2.6 4.7 - - + +
2885C GLN* 1.3 80.2 - - - +
2887C PRO* 1.3 68.1 - - + +
2888C VAL 3.1 0.2 + - - -
2889C GLY* 4.0 4.2 + - - -
2921C LEU* 2.3 74.2 + - + +
2922C ARG* 3.1 1.2 - - - +
2924C VAL* 3.1 13.9 - - + +
2925C GLU* 2.6 53.7 - - + +
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Residues in contact with PRO2887 (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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2884C LEU* 3.1 34.3 - - + +
2886C GLN* 1.3 83.7 - - + +
2888C VAL* 1.3 50.0 + - + -
2889C GLY 3.2 0.9 - - - -
2890C ILE* 2.5 37.5 + - + +
2891C ARG* 2.6 16.8 + - - -
2922C ARG* 3.2 42.8 - - - +
2930C TYR* 5.3 3.4 - - - +
3898C LEU* 5.3 13.5 - - + +
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Residues in contact with VAL2888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2857C CYS* 4.7 4.5 - - + +
2858C ILE* 4.2 15.0 - - + +
2861C ILE* 3.3 39.7 - - + +
2877C SER* 6.0 0.4 - - - +
2884C LEU 3.5 8.5 - - - +
2885C GLN* 2.9 41.6 + - + +
2887C PRO* 1.3 77.9 - - + +
2889C GLY* 1.3 60.9 + - - +
2891C ARG* 2.4 38.2 - - + +
2892C LEU 3.6 0.3 + - - -
3894C PRO* 4.4 7.2 - - + +
3895C GLU* 4.1 22.2 - - + +
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Residues in contact with GLY2889 (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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2861C ILE* 3.7 4.3 - - - -
2869C LEU* 3.2 30.6 - - - +
2872C ASP* 6.2 0.2 - - - -
2885C GLN 3.9 2.2 + - - -
2886C GLN 4.0 2.7 + - - -
2887C PRO 3.2 0.4 - - - -
2888C VAL* 1.3 78.1 - - - +
2890C ILE* 1.3 64.1 + - - +
2891C ARG 2.8 2.6 + - - -
2892C LEU 3.0 12.1 + - - -
2893C LEU* 3.1 11.6 + - - +
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Residues in contact with ILE2890 (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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2886C GLN 4.4 0.8 + - - -
2887C PRO* 2.5 24.8 + - + +
2889C GLY* 1.3 70.8 - - - +
2891C ARG* 1.3 61.9 + - - +
2893C LEU* 2.5 41.6 - - + +
2894C GLU* 3.1 14.8 + - + +
2918C PRO* 3.5 29.2 - - + +
2921C LEU* 3.3 47.9 - - + +
2922C ARG* 3.9 17.5 - - + +
3972C LEU* 6.1 3.6 - - + -
3974C MET* 6.4 1.1 - - + -
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Residues in contact with ARG2891 (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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2861C ILE* 4.6 9.2 - - + -
2887C PRO 2.6 10.4 + - - +
2888C VAL* 2.4 35.5 - - - +
2889C GLY 2.8 0.4 + - - -
2890C ILE* 1.3 78.1 - - - +
2892C LEU* 1.3 79.7 + - + +
2894C GLU* 3.1 10.2 + - - +
2895C GLU* 3.6 10.3 + - - +
3888C VAL* 5.8 0.4 - - - +
3894C PRO* 2.9 34.3 + - - +
3895C GLU* 5.1 0.6 - - - +
3897C PHE* 3.0 51.8 - - - +
3898C LEU* 3.7 24.9 - - - +
3972C LEU* 6.2 0.2 - - - +
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Residues in contact with LEU2892 (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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2861C ILE* 3.0 37.9 - - + +
2863C CYS 3.8 2.9 - - - +
2865C HIS 3.6 11.2 - - - +
2866C ALA 5.1 2.2 - - - +
2868C LEU* 3.5 22.2 - - + -
2869C LEU* 3.5 28.9 - - + -
2889C GLY 3.0 4.0 + - - -
2891C ARG* 1.3 92.5 - - + +
2893C LEU* 1.3 66.6 + - - +
2895C GLU* 3.0 27.6 + - + +
2896C ALA* 2.9 22.4 + - + -
2897C LEU* 3.3 7.7 + - + +
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Residues in contact with LEU2893 (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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2869C LEU* 4.8 0.8 - - - +
2889C GLY 3.1 6.7 + - - +
2890C ILE* 2.5 29.2 - - + +
2891C ARG 2.9 0.6 + - - -
2892C LEU* 1.3 76.5 - - - +
2894C GLU* 1.3 83.0 + - + +
2897C LEU* 3.4 22.4 - - + +
2898C LEU* 2.3 59.0 + - + -
2913C LYS 5.3 0.2 - - - +
2914C ALA* 3.1 27.6 - - - +
2915C ARG* 5.7 0.9 - - - -
2917C PRO* 5.0 3.8 - - + -
2918C PRO* 3.4 26.5 - - + -
3974C MET* 6.4 0.4 - - + -
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Residues in contact with GLU2894 (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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2890C ILE* 3.1 10.8 + - - +
2891C ARG 3.1 7.9 + - - +
2893C LEU* 1.3 97.3 - - + +
2895C GLU* 1.3 59.2 + - - +
2898C LEU* 2.8 36.8 - - + +
2902C PRO* 3.6 9.4 - - - +
3972C LEU* 3.3 18.4 - - - +
3973C PRO* 2.7 64.4 - - + +
3974C MET* 2.9 26.2 - - - +
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Residues in contact with GLU2895 (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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2891C ARG* 3.6 7.1 + - - +
2892C LEU* 3.0 43.8 + - - +
2894C GLU* 1.3 81.6 - - - +
2896C ALA* 1.3 77.8 + - + +
2898C LEU 2.8 11.7 - - - +
2899C ARG* 5.0 1.4 - - - +
2902C PRO* 4.6 3.3 - - - +
3973C PRO* 4.8 4.9 - - + +
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Residues in contact with ALA2896 (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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2865C HIS 5.5 3.8 - - - +
2866C ALA* 4.3 7.9 - - + -
2892C LEU* 2.9 4.4 + - + +
2895C GLU* 1.3 94.2 - - + +
2897C LEU* 1.3 72.1 + - - +
2898C LEU 3.2 6.8 - - - -
2899C ARG* 3.5 26.3 + - - +
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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