Contacts of the strand formed by residues 3039 - 3047 (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 ASP3039 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3038D MET* 1.3 75.6 - - - +
3040D LYS* 1.3 74.2 + - + +
3041D PRO* 3.3 3.4 - - - -
3055D ALA* 3.3 2.6 - - - -
3056D GLU* 2.7 50.7 + - + +
3058D ASP* 5.4 4.5 + - - -
3059D GLY 5.8 1.0 + - - -
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Residues in contact with LYS3040 (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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3039D ASP* 1.3 79.5 - - + +
3041D PRO* 1.3 72.5 - - - +
3042D VAL* 3.3 13.5 + - + +
3054D ARG* 3.5 8.7 + - - +
3055D ALA* 4.0 2.3 - - - -
3056D GLU* 3.6 36.6 + - + +
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Residues in contact with PRO3041 (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* 3.3 27.6 - - + +
3036D ALA* 4.2 11.2 - - + +
3038D MET 3.5 10.8 - - - +
3039D ASP 3.3 5.8 - - - -
3040D LYS* 1.3 88.3 - - - +
3042D VAL* 1.3 65.8 + - - +
3053D TRP* 3.6 21.8 - - + -
3054D ARG 3.2 8.7 - - - +
3055D ALA* 4.2 2.0 - - + -
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Residues in contact with VAL3042 (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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3040D LYS* 3.5 12.3 - - + +
3041D PRO* 1.3 80.0 - - - +
3043D LYS* 1.3 76.6 + - - +
3044D LEU* 3.3 10.5 - - + +
3053D TRP* 3.3 6.7 - - - -
3054D ARG* 2.8 52.9 + - - +
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Residues in contact with LYS3043 (chain D).
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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3042D VAL* 1.3 85.5 - - - +
3044D LEU* 1.3 65.2 + - - +
3045D ALA* 4.4 6.7 - - - +
3046D SER* 4.1 26.8 - - - -
3051D THR* 5.7 2.2 - - - -
3052D SER 4.1 2.2 - - - +
3053D TRP* 3.3 50.5 - - + +
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Residues in contact with LEU3044 (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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3011D LEU* 3.5 30.8 - - + +
3015D ASP* 4.0 23.0 - - + +
3016D LEU* 5.0 0.4 - - + -
3042D VAL* 3.3 22.2 - - + +
3043D LYS* 1.3 79.7 - - - +
3045D ALA* 1.3 62.9 + - - +
3052D SER* 2.8 20.2 + - - +
3053D TRP 3.9 6.3 - - - +
3054D ARG* 3.3 29.6 - - + +
3063D ILE* 3.7 30.3 - - + -
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Residues in contact with ALA3045 (chain D).
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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3009D LEU 3.6 23.3 - - - +
3010D GLY 3.8 13.7 - - - +
3011D LEU* 3.9 3.1 - - + -
3043D LYS* 4.4 9.1 - - - +
3044D LEU* 1.3 83.1 - - - +
3046D SER* 1.3 66.1 + - - +
3047D HIS* 4.2 8.5 - - + -
3050D PHE 4.4 0.4 - - - -
3051D THR* 3.5 0.9 - - - -
3052D SER* 2.9 34.0 + - - +
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Residues in contact with SER3046 (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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6029B GLU* 5.4 2.3 - - - +
3043D LYS* 4.1 18.6 - - - -
3045D ALA* 1.3 83.6 - - - +
3047D HIS* 1.3 71.5 + - - +
3048D ARG 5.0 1.6 + - - -
3050D PHE 3.5 7.6 - - - -
3051D THR* 3.0 28.0 - - - +
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Residues in contact with HIS3047 (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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6029B GLU* 5.2 9.4 - - - -
3008D HIS 3.4 20.7 + - - +
3009D LEU 3.2 24.2 + - - +
3010D GLY* 4.0 13.9 - - - -
3045D ALA* 4.2 12.3 - - + -
3046D SER* 1.3 82.3 + - - +
3048D ARG* 1.3 78.1 + - + +
3049D GLU 3.1 0.2 + - - -
3050D PHE* 2.7 27.5 + - - +
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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