Contacts of the helix formed by residues 2963 - 2975 (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 SER2963 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2960C GLU* 2.2 24.2 + - - +
2962C ARG* 1.3 87.1 + - - +
2964C ASP* 1.3 61.2 + - - -
2965C TYR 3.0 2.5 - - - -
2966C SER* 2.3 31.7 + - - -
2967C GLU* 2.6 26.2 + - - -
3010C SER* 5.5 1.7 + - - -
3253C SER* 4.7 2.9 - - - -
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Residues in contact with ASP2964 (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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2955C SER* 3.3 9.7 + - - +
2958C LEU* 5.3 12.6 - - + +
2960C GLU* 2.9 31.1 + - + +
2963C SER* 1.3 73.4 - - - +
2965C TYR* 1.3 50.1 + - - +
2967C GLU* 4.0 6.5 - - - +
2968C ALA* 2.7 35.6 + - - +
3252C PHE* 4.9 13.3 - - - +
3253C SER* 4.5 4.5 + - - -
3289C ARG* 5.9 1.4 + - - -
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Residues in contact with TYR2965 (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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2952C ILE* 3.4 34.1 - - + -
2955C SER* 2.8 23.7 + - - +
2960C GLU* 3.6 8.4 - - + +
2963C SER 2.8 3.8 - - - +
2964C ASP* 1.3 71.5 - - - +
2966C SER* 1.3 59.3 + - - +
2968C ALA* 2.1 34.2 + - - -
2969C ALA* 2.7 31.2 + - + -
2994C TRP* 5.1 1.6 - + - -
2995C GLU* 2.7 38.8 + - - -
2998C SER* 3.3 6.0 - - - -
2999C LEU* 3.4 26.2 - - + +
3002C TYR* 3.0 48.7 - + + -
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Residues in contact with SER2966 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2962C ARG 3.7 16.3 + - - -
2963C SER* 2.3 20.4 + - - -
2965C TYR* 1.3 84.0 - - - +
2967C GLU* 1.3 62.5 + - - -
2970C LYS* 2.2 51.1 + - - +
2999C LEU* 3.5 21.8 - - - +
3003C ASN* 5.5 0.7 - - - -
3010C SER* 5.4 5.3 + - - -
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Residues in contact with GLU2967 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2963C SER* 2.6 26.3 + - - +
2964C ASP* 4.2 6.3 - - - +
2965C TYR 2.8 1.6 - - - -
2966C SER* 1.3 76.5 + - - +
2968C ALA* 1.3 56.2 + - - +
2970C LYS* 5.9 2.0 - - - +
2971C GLN* 2.7 41.3 + - - +
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Residues in contact with ALA2968 (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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2951C GLN* 4.4 4.2 - - + +
2952C ILE* 3.5 25.1 - - + +
2955C SER* 4.4 2.0 - - - +
2964C ASP 2.7 22.1 + - - +
2965C TYR* 2.1 21.6 + - - +
2967C GLU* 1.3 73.5 - - - +
2969C ALA* 1.3 55.4 + - - +
2971C GLN* 3.4 3.8 - - - +
2972C TYR* 3.1 20.4 + - - +
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Residues in contact with ALA2969 (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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2952C ILE* 3.3 17.5 - - + -
2965C TYR* 2.7 35.0 + - + -
2968C ALA* 1.3 73.4 - - - +
2970C LYS* 1.3 54.3 + - - +
2971C GLN 3.0 3.4 - - - -
2972C TYR* 2.6 42.6 + - + +
2973C ASP 4.2 0.5 + - - -
2995C GLU* 3.0 24.0 - - - +
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Residues in contact with LYS2970 (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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2965C TYR 3.8 0.2 + - - -
2966C SER* 2.2 51.7 + - - +
2967C GLU* 5.9 2.0 - - - +
2969C ALA* 1.3 77.4 - - - +
2971C GLN* 1.3 57.7 + - + +
2972C TYR 3.1 0.3 + - - -
2973C ASP* 3.9 1.4 + - - +
2974C GLU* 2.4 69.4 + - + +
2999C LEU* 3.6 26.8 - - + +
3013C TYR* 2.8 43.8 + - - -
3014C CYS* 6.0 0.4 - - - -
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Residues in contact with GLN2971 (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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2966C SER 4.5 1.0 + - - -
2967C GLU* 2.7 43.8 + - - +
2968C ALA 3.4 6.9 - - - +
2970C LYS* 1.3 74.3 + - - +
2972C TYR* 1.3 66.3 + - + +
2974C GLU* 3.6 9.4 - - + -
2975C ALA* 2.6 36.3 + - + +
2979C GLN* 3.2 15.1 + - - +
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Residues in contact with TYR2972 (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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2948C GLY* 2.7 38.6 + - - -
2951C GLN* 2.2 32.0 + - - -
2952C ILE* 3.0 11.5 - - + +
2968C ALA 3.1 21.8 + - - -
2969C ALA* 2.6 31.7 + - + +
2971C GLN* 1.3 79.0 - - + +
2973C ASP* 1.3 58.4 + - - +
2977C ASN* 2.9 21.8 + - - +
2979C GLN* 4.7 0.7 - - - -
2980C ASP* 2.6 37.2 - - - +
2991C LYS* 3.6 19.1 - - - +
2995C GLU* 3.0 28.0 - - - +
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Residues in contact with ASP2973 (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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2969C ALA 4.2 0.2 + - - -
2970C LYS 3.9 2.1 + - - +
2972C TYR* 1.3 80.2 - - - +
2974C GLU* 1.3 57.1 + - - +
2976C LEU* 2.5 29.4 + - - +
2977C ASN* 4.1 5.3 + - - +
2991C LYS* 4.2 0.9 + - - -
2992C ASP* 2.6 56.5 - - - +
2995C GLU* 3.2 15.9 - - + +
2996C LEU* 2.7 33.8 + - + +
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Residues in contact with GLU2974 (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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2970C LYS* 2.4 66.9 + - + +
2971C GLN* 3.6 5.6 - - + -
2973C ASP* 1.3 79.1 - - - +
2975C ALA* 1.3 61.3 + - - +
2976C LEU* 3.2 1.2 + - - +
2999C LEU* 5.6 1.2 - - - +
3013C TYR* 4.1 8.8 + - - -
3017C ALA* 5.9 2.3 - - - +
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Residues in contact with ALA2975 (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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2971C GLN* 2.6 29.4 + - + +
2974C GLU* 1.3 71.9 - - - +
2976C LEU* 1.3 54.9 - - - +
2977C ASN 3.6 0.2 - - - +
2978C LYS* 2.1 54.0 + - + +
2979C GLN* 3.1 28.0 - - - +
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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