Contacts of the strand formed by residues 3050 - 3058 (chain C) in PDB entry 1D1Z
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 TYR3050 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3046C LEU* 3.5 4.6 - - - -
3047C TYR 2.8 33.6 + - - +
3048C HIS* 3.4 17.7 - - + -
3049C GLY* 1.3 84.3 - - - +
3051C ILE* 1.3 64.3 + - - +
3052C TYR* 3.5 23.9 - - + -
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Residues in contact with ILE3051 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3017C GLU* 4.1 39.3 - - + +
3020C LEU* 3.6 32.8 - - + -
3021C LEU* 4.0 18.2 - - + -
3044C CYS* 4.2 16.2 - - + -
3045C VAL 3.5 3.8 - - - +
3046C LEU* 3.7 21.5 - - + -
3050C TYR* 1.3 75.7 - - - +
3052C TYR* 1.3 70.7 + - - +
3053C THR* 3.9 18.0 + - - +
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Residues in contact with TYR3052 (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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3043C LEU 3.5 1.9 - - - +
3044C CYS* 3.3 4.0 - - - -
3045C VAL* 2.8 39.1 + - + +
3047C TYR* 3.6 40.4 + + + -
3050C TYR* 3.5 29.0 - + + +
3051C ILE* 1.3 76.2 - - - +
3053C THR* 1.3 60.4 + - - +
3054C TYR* 3.6 34.1 - + + +
3095C VAL* 3.6 31.0 - - + +
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Residues in contact with THR3053 (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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3017C GLU* 4.3 8.3 + - - -
3032C ARG* 3.8 13.4 + - - +
3042C CYS* 3.7 32.8 - - + -
3043C LEU 3.5 2.9 - - - -
3044C CYS* 4.1 6.6 - - - -
3051C ILE* 3.9 15.8 + - - +
3052C TYR* 1.3 73.7 + - - +
3054C TYR* 1.3 69.4 + - - +
3055C ARG* 4.1 6.3 + - + +
5003C SO4 4.4 4.9 - - - +
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Residues in contact with TYR3054 (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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3042C CYS* 3.6 2.1 - - - -
3043C LEU* 2.8 57.5 + - + +
3045C VAL* 4.1 14.8 - - + -
3052C TYR* 3.6 32.4 - + + +
3053C THR* 1.3 79.6 - - - +
3055C ARG* 1.3 65.3 + - - +
3056C VAL 3.4 0.3 + - - -
3066C ALA* 4.8 9.6 - - + -
3067C GLU 3.7 21.8 - - - +
3068C THR* 4.5 6.1 - - - -
3069C ALA 5.6 0.2 - - - -
3093C GLY 4.6 4.3 - - - -
3094C ILE* 3.6 38.3 - - + -
3095C VAL* 3.0 33.2 + - + +
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Residues in contact with ARG3055 (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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3034C SER* 3.8 2.4 + - - -
3036C SER* 3.4 21.7 + - - -
3037C VAL* 4.3 15.8 - - - +
3040C VAL* 3.8 21.3 - - + -
3041C TYR 3.4 2.0 - - - -
3042C CYS* 3.7 16.9 - - - +
3053C THR* 4.1 6.4 + - + +
3054C TYR* 1.3 72.8 - - - +
3056C VAL* 1.3 58.8 + - - +
3057C SER 4.2 0.4 + - - -
3065C SER 3.9 0.5 - - - +
3066C ALA* 3.3 2.4 - - - -
3067C GLU* 2.9 64.1 + - - +
5003C SO4 3.0 33.5 + - - -
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Residues in contact with VAL3056 (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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3031C LEU* 4.3 5.8 - - + -
3040C VAL* 3.5 0.9 - - - +
3041C TYR* 2.8 51.9 + - + +
3043C LEU* 3.8 20.2 - - + +
3054C TYR 3.8 9.6 - - - +
3055C ARG* 1.3 78.3 - - - +
3057C SER* 1.3 66.3 + - - +
3064C TRP* 3.7 11.4 - - + -
3065C SER 3.3 7.9 - - - +
3066C ALA* 3.9 17.0 - - + -
3080C ILE* 3.6 30.5 - - + -
3083C LEU* 4.1 11.2 - - + -
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Residues in contact with SER3057 (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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3039C GLY 5.5 0.2 - - - -
3040C VAL* 3.6 29.2 - - - +
3055C ARG 4.2 0.9 + - - -
3056C VAL* 1.3 77.6 - - - +
3058C GLN* 1.3 64.7 + - - +
3059C THR* 4.2 0.9 + - - +
3063C SER 3.6 1.0 - - - +
3064C TRP* 3.4 9.5 - - - -
3065C SER* 3.0 36.4 + - - +
3067C GLU* 4.6 12.2 + - - +
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Residues in contact with GLN3058 (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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3057C SER* 1.3 78.8 - - - +
3059C THR* 1.3 68.3 + - - +
3062C GLY* 3.2 39.8 + - - +
3063C SER 2.9 4.5 - - - -
3064C TRP* 3.4 43.8 - - + +
3078C ARG 5.5 0.2 + - - -
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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