Contacts of the helix formed by residues 2989 - 3007 (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 ALA2989 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2987C THR 3.6 1.2 + - - -
2988C GLU* 1.3 84.1 - - + +
2990C GLU* 1.3 62.1 - - - +
2991C LYS 3.1 1.3 - - - +
2992C ASP* 2.5 9.3 + - - +
2993C PHE* 2.0 69.0 + - + -
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Residues in contact with GLU2990 (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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2912C GLY* 3.8 23.3 - - - -
2915C ARG* 6.0 0.2 - - - -
2916C LEU* 3.5 43.0 - - + +
2919C ASP* 4.9 4.0 - - - +
2939C LEU* 5.7 1.1 - - - -
2942C ILE* 4.4 12.9 - - + +
2988C GLU* 4.2 8.0 - - - +
2989C ALA* 1.3 79.8 + - - +
2991C LYS* 1.3 57.2 + - - +
2993C PHE* 3.3 23.0 - - + -
2994C TRP* 2.8 35.1 + - - +
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Residues in contact with LYS2991 (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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2939C LEU* 5.1 2.0 - - - -
2942C ILE* 3.8 13.1 - - + +
2944C THR* 4.7 4.3 - - + -
2945C SER* 3.0 40.4 - - - +
2948C GLY* 6.1 0.2 - - - -
2949C THR* 3.6 17.7 - - - +
2972C TYR* 3.6 17.4 - - - +
2973C ASP* 4.2 2.2 + - - -
2977C ASN* 4.7 3.0 + - - -
2987C THR* 3.0 31.0 - - + +
2989C ALA 3.1 1.2 - - - +
2990C GLU* 1.3 76.6 - - - +
2992C ASP* 1.3 58.0 + - - +
2994C TRP* 4.1 5.8 - - + -
2995C GLU* 2.3 82.0 + - - +
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Residues in contact with ASP2992 (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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2973C ASP* 2.6 39.8 - - - +
2976C LEU* 5.3 4.0 - - - +
2977C ASN* 3.3 15.9 + - - +
2981C TRP* 5.8 0.7 - - - -
2987C THR* 3.0 23.1 - - - +
2988C GLU 2.6 23.7 - - - +
2989C ALA* 2.5 15.0 + - - +
2991C LYS* 1.3 79.2 - - - +
2993C PHE* 1.3 68.4 + - + +
2996C LEU* 2.8 7.6 + - - +
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Residues in contact with PHE2993 (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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2916C LEU* 4.2 16.4 - - + -
2989C ALA* 2.0 53.8 + - + +
2990C GLU* 3.3 39.3 - - + -
2992C ASP* 1.3 74.0 - - + +
2994C TRP* 1.3 64.5 + - + +
2996C LEU* 2.9 9.7 + - - +
2997C ALA* 2.9 18.4 + - - +
3035C PHE* 6.0 9.4 - + - -
3036C TYR* 6.3 4.3 - - + -
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Residues in contact with TRP2994 (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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2916C LEU* 5.5 3.6 - - + -
2919C ASP* 4.5 20.6 - - + +
2923C TRP* 3.5 37.4 - + - +
2934C GLY 4.2 9.1 + - - -
2935C GLU* 3.0 38.8 - - + +
2939C LEU* 3.3 28.0 - - + +
2949C THR* 3.8 13.2 - - + -
2952C ILE* 4.1 11.4 - - + -
2965C TYR* 5.1 0.2 - + - -
2990C GLU* 2.8 16.9 + - - +
2991C LYS* 4.1 3.8 - - + -
2993C PHE* 1.3 79.9 - - + +
2995C GLU* 1.3 79.1 + - + +
2997C ALA* 4.7 1.6 - - - -
2998C SER* 1.9 62.8 + - - +
3002C TYR* 4.9 4.7 - - - -
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Residues in contact with GLU2995 (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* 3.9 1.4 - - - +
2965C TYR* 2.7 41.3 + - - -
2969C ALA* 3.0 9.6 - - - +
2972C TYR* 3.0 28.6 - - + -
2973C ASP* 3.0 29.2 - - + +
2991C LYS* 2.3 58.4 + - - +
2993C PHE 3.0 0.4 - - - -
2994C TRP* 1.3 102.1 - - - +
2996C LEU* 1.3 55.9 + - - +
2998C SER* 3.0 0.5 - - - -
2999C LEU* 3.0 13.5 + - - +
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Residues in contact with LEU2996 (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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2973C ASP* 2.7 21.3 + - + +
2992C ASP 2.8 15.5 + - - +
2993C PHE* 2.9 2.6 + - - +
2995C GLU* 1.3 71.9 - - - +
2997C ALA* 1.3 59.4 + - - +
2998C SER 2.9 1.1 - - - -
2999C LEU* 2.4 43.0 + - + +
3000C ASP* 2.9 14.8 + - + +
3014C CYS* 5.9 1.1 - - + +
3017C ALA* 4.5 28.5 - - + +
3018C SER* 5.0 9.9 - - - +
3036C TYR* 6.1 3.6 - - + +
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Residues in contact with ALA2997 (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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2923C TRP* 3.5 17.5 - - + -
2993C PHE 2.9 18.6 + - - +
2994C TRP* 4.7 0.4 - - - -
2996C LEU* 1.3 74.4 - - - +
2998C SER* 1.3 67.5 + - - +
3000C ASP* 4.5 2.7 - - - +
3001C CYS* 2.9 28.9 + - - -
3036C TYR* 3.6 32.9 - - + +
3039C THR* 4.8 3.1 - - + -
3043C TYR* 4.3 9.0 - - - +
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Residues in contact with SER2998 (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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2923C TRP* 3.3 13.1 - - - -
2965C TYR* 3.3 5.6 - - - -
2994C TRP* 1.9 60.1 + - - -
2995C GLU* 3.0 8.7 - - - -
2997C ALA* 1.3 77.8 - - - +
2999C LEU* 1.3 67.9 + - - -
3000C ASP 2.8 0.3 + - - -
3001C CYS* 2.9 7.6 + - - -
3002C TYR* 2.8 36.5 - - - -
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Residues in contact with LEU2999 (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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2962C ARG 5.5 0.7 - - - +
2965C TYR* 3.4 29.6 - - + -
2966C SER* 3.5 24.9 - - - +
2970C LYS* 3.6 37.9 - - + +
2974C GLU* 5.6 1.6 - - - +
2995C GLU* 3.0 7.0 + - - +
2996C LEU* 2.4 30.7 + - + +
2998C SER* 1.3 76.0 - - - +
3000C ASP* 1.3 61.1 + - + +
3002C TYR* 2.9 29.7 + - + +
3003C ASN* 4.6 2.1 + - - +
3014C CYS* 4.2 23.8 - - + -
3017C ALA* 6.4 1.3 - - + -
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Residues in contact with ASP3000 (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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2996C LEU* 2.9 16.3 + - + +
2997C ALA* 4.2 2.9 - - - +
2999C LEU* 1.3 74.1 - - + +
3001C CYS* 1.3 56.7 + - - +
3002C TYR 2.6 17.2 + - - -
3003C ASN* 3.4 4.0 + - - +
3004C HIS* 2.9 19.5 + - - +
3010C SER 3.7 5.2 - - - +
3011C LEU* 4.3 0.9 - - - -
3014C CYS* 3.1 33.6 - - + +
3015C SER* 3.0 24.9 + - - -
3018C SER* 4.5 0.9 - - - -
3043C TYR* 3.0 37.7 - - + +
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Residues in contact with CYS3001 (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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2923C TRP* 3.3 31.2 - - + -
2926C LEU* 5.2 6.6 - - + +
2997C ALA* 2.9 28.7 + - - +
2998C SER 2.9 3.3 + - - +
3000C ASP* 1.3 75.0 - - - +
3002C TYR* 1.3 60.4 + - + +
3004C HIS* 3.3 15.4 - - + +
3005C LEU* 2.9 34.2 + - + +
3039C THR* 5.0 4.9 - - - -
3043C TYR* 3.2 26.5 - - - -
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Residues in contact with TYR3002 (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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2923C TRP* 5.5 2.7 - + - -
2931C ARG* 5.6 13.0 - - + -
2956C ALA* 6.1 3.6 - - + -
2960C GLU 4.5 8.1 - - - -
2961C ALA* 2.8 37.1 - - - +
2962C ARG 4.3 4.0 - - - +
2965C TYR* 3.0 60.6 - + + -
2966C SER 5.3 0.2 - - - -
2994C TRP* 4.9 4.2 - - - -
2998C SER* 2.8 43.2 + - - -
2999C LEU* 2.9 17.9 - - + +
3000C ASP 2.6 6.3 + - - -
3001C CYS* 1.3 82.5 - - + +
3003C ASN* 1.3 60.3 + - - +
3005C LEU* 3.3 3.3 + - - +
3006C ALA 2.8 16.5 + - - -
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Residues in contact with ASN3003 (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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2961C ALA 2.1 28.8 + - - -
2962C ARG* 2.7 67.1 - - - +
2966C SER* 5.5 0.2 - - - -
2999C LEU 4.6 1.9 + - - +
3000C ASP 3.4 2.9 + - - +
3002C TYR* 1.3 72.6 - - - +
3004C HIS* 1.3 60.4 + - - +
3006C ALA* 2.8 5.5 + - - +
3007C GLU* 2.3 40.4 + - - +
3010C SER* 3.1 29.7 - - - -
3011C LEU* 3.7 7.7 - - - +
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Residues in contact with HIS3004 (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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3000C ASP* 2.9 27.4 + - - +
3001C CYS* 3.3 16.4 - - - +
3003C ASN* 1.3 76.3 - - - +
3005C LEU* 1.3 66.6 + - + +
3011C LEU* 3.6 10.4 - - + +
3042C PRO* 3.2 28.8 - - + +
3043C TYR* 3.0 36.8 - + + -
3046C ARG* 2.3 75.9 + - + +
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Residues in contact with LEU3005 (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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2926C LEU* 3.8 36.8 - - + -
2961C ALA* 5.3 3.8 - - + -
3001C CYS* 2.9 20.1 + - + +
3002C TYR* 3.6 7.4 - - - +
3004C HIS* 1.3 91.7 - - + +
3006C ALA* 1.3 55.0 + - + +
3046C ARG* 2.1 32.9 + - - +
3177C ASN* 3.4 34.8 + - - +
3180C ASP* 4.7 7.6 - - - +
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Residues in contact with ALA3006 (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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2961C ALA* 3.2 21.5 - - + +
2962C ARG* 2.1 34.5 + - - +
3002C TYR 2.8 5.2 + - - +
3003C ASN* 2.8 34.3 + - - +
3005C LEU* 1.3 71.9 - - - +
3007C GLU* 1.3 63.4 + - - +
3180C ASP* 4.9 2.0 - - - -
3254C LEU* 3.5 21.1 - - + +
3257C LYS* 3.9 2.1 + - - -
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Residues in contact with GLU3007 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2962C ARG* 2.5 23.7 + - - -
3003C ASN* 2.3 30.7 + - - +
3005C LEU 3.3 1.2 - - - -
3006C ALA* 1.3 70.8 - - - +
3008C TRP* 1.3 64.5 + - - +
3011C LEU* 3.3 11.3 - - - +
3046C ARG* 2.7 58.2 + - - +
3047C SER 3.7 0.5 - - - +
3049C LEU* 3.0 17.5 - - + +
3050C LYS* 2.3 42.6 + - + +
3180C ASP* 6.3 3.1 - - + -
3184C THR* 5.8 6.5 - - + -
3257C LYS* 5.1 5.8 - - - +
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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