Contacts of the strand formed by residues 3041 - 3047 (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 TYR3041 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3007C TYR* 3.5 38.0 + + - -
3031C LEU* 3.9 23.8 - - + -
3032C ARG 3.3 16.4 - - - +
3033C ASP* 3.6 11.0 - - - -
3034C SER 3.9 0.4 - - - +
3039C GLY* 3.7 20.5 + - - -
3040C VAL* 1.3 81.6 - - - +
3042C CYS* 1.3 67.9 - - - +
3055C ARG* 3.4 5.7 - - - -
3056C VAL* 2.8 35.5 + - + +
3064C TRP* 3.5 39.7 - + - -
3080C ILE* 6.4 0.2 - - + -
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Residues in contact with CYS3042 (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* 3.3 6.8 - - - -
3032C ARG* 2.8 52.1 + - + -
3034C SER* 3.8 12.3 - - - -
3041C TYR* 1.3 79.5 - - - +
3043C LEU* 1.3 60.4 + - - +
3044C CYS* 3.6 5.2 + - - -
3053C THR* 3.7 20.2 - - + -
3054C TYR 3.6 3.8 - - - -
3055C ARG* 3.7 16.4 - - - -
5003C SO4 3.4 33.2 - - - -
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Residues in contact with LEU3043 (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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3029C TYR* 4.1 8.7 - - + -
3030C LEU 3.6 13.7 - - - +
3031C LEU* 3.8 7.2 - - + +
3041C TYR 4.2 0.2 - - - -
3042C CYS* 1.3 70.7 - - - +
3044C CYS* 1.3 59.4 + - - +
3045C VAL* 4.2 6.1 - - + -
3052C TYR 3.5 1.9 - - - +
3053C THR* 3.5 1.2 - - - -
3054C TYR* 2.8 59.6 + - + +
3056C VAL* 3.8 19.7 - - + +
3066C ALA* 5.1 2.9 - - + -
3083C LEU* 4.8 12.1 - - + -
3084C ILE* 4.0 22.0 - - + -
3087C PHE* 4.8 10.5 - - + -
3094C ILE* 4.9 3.4 - - + -
3098C LEU* 4.0 34.1 - - + -
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Residues in contact with CYS3044 (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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3016C GLY* 6.2 1.1 - - - -
3017C GLU* 5.9 2.9 - - + -
3020C LEU* 3.5 22.0 - - + +
3029C TYR* 3.1 6.8 - - - +
3030C LEU* 2.9 40.1 + - + +
3032C ARG* 3.4 35.7 - - - -
3042C CYS* 3.6 21.1 - - - -
3043C LEU* 1.3 74.7 - - - +
3045C VAL* 1.3 61.9 - - - +
3051C ILE* 4.2 9.6 - - + -
3052C TYR 3.3 3.8 - - - -
3053C THR* 4.1 10.1 - - - -
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Residues in contact with VAL3045 (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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3020C LEU* 4.2 2.2 - - - +
3027C GLY* 4.2 7.4 - - - -
3028C SER 3.4 9.4 - - - +
3043C LEU* 4.2 8.1 - - + -
3044C CYS* 1.3 80.2 - - - +
3046C LEU* 1.3 64.8 + - - +
3050C TYR 3.6 0.5 - - - +
3051C ILE* 3.5 2.6 - - - -
3052C TYR* 2.8 40.4 + - + +
3054C TYR* 4.1 20.4 - - + -
3094C ILE* 4.6 2.2 - - + -
3095C VAL* 5.3 2.9 - - + -
3096C ILE* 3.9 31.4 - - + +
3097C PRO 4.9 0.2 - - - +
3098C LEU* 3.5 32.1 - - + -
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Residues in contact with LEU3046 (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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3020C LEU* 3.4 26.9 - - + +
3021C LEU* 3.8 19.5 - - + -
3023C THR* 3.8 0.9 - - - +
3024C GLY* 3.8 10.8 - - - +
3025C LEU 3.5 37.2 - - - +
3026C ASP* 3.5 1.1 - - - +
3027C GLY* 2.8 29.5 + - - -
3028C SER* 3.0 15.9 + - - +
3045C VAL* 1.3 72.8 - - - +
3047C TYR* 1.3 65.7 + - - +
3048C HIS 5.1 0.2 - - - +
3049C GLY* 3.9 17.0 - - - +
3050C TYR 3.5 15.0 - - - +
3051C ILE* 3.7 22.0 - - + -
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Residues in contact with TYR3047 (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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3026C ASP* 3.6 12.3 - - - -
3045C VAL 3.9 0.2 + - - -
3046C LEU* 1.3 76.8 - - - +
3048C HIS* 1.3 115.7 + + + +
3049C GLY 3.1 0.4 - - - -
3050C TYR* 2.8 28.6 + - - +
3052C TYR* 3.6 20.5 + - + -
3095C VAL* 3.6 41.3 - - + -
3096C ILE* 3.8 38.8 - - + +
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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