Contacts of the strand formed by residues 3050 - 3057 (chain D) in PDB entry 1Y1S
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 PHE3050 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6069B ILE* 3.9 24.0 - - + -
3008D HIS* 4.0 29.2 - + + -
3009D LEU* 4.2 23.3 - - + +
3045D ALA 4.2 0.7 - - - +
3046D SER* 3.5 2.9 + - - -
3047D HIS* 2.7 32.1 + - - +
3048D ARG* 3.3 9.4 - - + -
3049D GLU* 1.3 84.0 - - + +
3051D THR* 1.3 62.1 + - - +
3052D SER* 3.8 2.9 + - - -
3065D CYS* 4.4 5.2 - - - -
3066D SER* 3.5 21.5 - - - +
3067D THR* 3.6 13.7 - - - -
3073D SER* 3.1 37.7 - - - -
3076D ILE* 4.0 13.0 - - + -
3077D ALA* 3.9 13.9 - - + -
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Residues in contact with THR3051 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3028D PRO* 3.2 43.4 + - + +
3031D VAL* 3.3 16.9 - - - +
3043D LYS* 5.7 2.5 - - - -
3045D ALA 3.5 4.9 - - - -
3046D SER* 3.0 27.1 - - - +
3048D ARG 4.8 4.3 - - - +
3049D GLU 4.7 0.7 - - - -
3050D PHE* 1.3 75.8 - - - +
3052D SER* 1.3 59.7 + - - +
3053D TRP* 4.8 5.5 + - - -
3065D CYS* 3.5 0.6 - - - -
3066D SER* 3.0 26.3 + - - -
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Residues in contact with SER3052 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3009D LEU* 4.8 1.5 + - - -
3011D LEU* 3.4 34.5 - - - +
3044D LEU* 2.8 28.5 + - - -
3045D ALA* 2.9 27.8 + - - +
3050D PHE 3.8 2.4 + - - -
3051D THR* 1.3 73.9 - - - +
3053D TRP* 1.3 70.1 + - - +
3063D ILE* 5.3 2.0 - - - -
3064D VAL 3.4 3.1 - - - -
3065D CYS* 4.1 18.2 - - - +
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Residues in contact with TRP3053 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3031D VAL* 3.4 30.5 - - + +
3032D GLU* 3.2 37.9 - - + +
3035D ALA* 3.8 18.6 - - + -
3041D PRO* 3.6 24.5 - - + -
3042D VAL* 3.3 23.6 - - - -
3043D LYS* 3.3 54.4 - - + +
3044D LEU* 3.9 4.5 - - - -
3051D THR* 4.8 5.1 + - - -
3052D SER* 1.3 85.3 - - - +
3054D ARG* 1.3 59.6 + - - +
3063D ILE* 3.4 9.5 - - - +
3064D VAL* 2.9 31.2 + - + +
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Residues in contact with ARG3054 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3015D ASP* 3.0 29.3 + - - +
3016D LEU 3.2 17.9 - - - +
3017D GLN* 3.4 33.0 + - - +
3035D ALA* 5.1 0.4 - - - -
3040D LYS 3.5 4.8 + - - +
3041D PRO* 3.2 4.2 - - - +
3042D VAL* 2.8 53.6 + - - +
3044D LEU* 3.3 30.8 - - + +
3053D TRP* 1.3 76.5 - - - +
3055D ALA* 1.3 71.2 + - - +
3056D GLU* 6.3 0.8 - - - +
3061D ALA* 4.5 3.0 - - - +
3062D VAL 3.4 12.1 - - - +
3063D ILE* 3.8 10.1 - - + -
3064D VAL* 5.9 0.2 - - - -
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Residues in contact with ALA3055 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3035D ALA* 3.9 15.0 - - - +
3038D MET* 3.7 34.1 - - + -
3039D ASP 3.3 13.5 - - - +
3040D LYS 4.0 4.0 - - - -
3041D PRO* 4.2 1.8 - - + -
3054D ARG* 1.3 81.2 + - - +
3056D GLU* 1.3 61.7 + - - +
3061D ALA* 3.2 7.1 - - - +
3062D VAL* 2.7 33.8 + - - +
3064D VAL* 5.4 0.2 - - + -
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Residues in contact with GLU3056 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3038D MET* 3.5 6.2 - - - +
3039D ASP* 2.7 50.6 + - + +
3040D LYS* 3.6 35.5 + - + +
3054D ARG* 6.3 0.4 - - - +
3055D ALA* 1.3 81.6 - - - +
3057D LEU* 1.3 62.0 + - - +
3058D ASP 4.1 0.2 - - - -
3059D GLY* 3.2 32.6 + - - +
3060D LYS 3.1 13.0 - - - +
3061D ALA* 4.1 5.9 - - + +
3062D VAL* 4.9 1.1 - - - -
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Residues in contact with LEU3057 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3038D MET* 4.0 26.9 - - + -
3056D GLU* 1.3 73.2 - - - +
3058D ASP* 1.3 68.3 + - - +
3059D GLY 3.2 0.4 - - - -
3060D LYS* 2.7 38.6 + - - +
3062D VAL* 4.0 4.2 - - + +
3246D VAL* 3.5 21.3 - - + +
3249D ALA* 4.0 9.2 - - + -
3250D ARG* 3.5 56.1 - - + +
3253D LEU* 3.3 22.9 - - + +
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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