Contacts of the strand formed by residues 5088 - 5097 (chain E) 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 THR5088 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5020E GLN 3.0 4.1 + - - -
5021E LEU* 3.2 34.1 - - + +
5022E ALA 2.9 25.6 + - - +
5086E ILE* 3.4 4.0 - - - +
5087E ARG* 1.3 80.1 - - - +
5089E PHE* 1.3 67.3 + - - +
5090E LEU* 4.5 2.2 - - + -
5136E CYS* 3.6 28.7 - - - -
5212E ARG* 2.7 39.7 + - - +
5252E LEU* 4.1 3.8 - - + -
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Residues in contact with PHE5089 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5022E ALA* 3.5 4.0 - - + +
5024E VAL* 4.3 13.9 - - + -
5078E VAL* 3.6 31.0 - - + -
5081E LEU* 3.5 30.5 - - + -
5082E ALA* 4.1 2.9 - - + -
5086E ILE* 3.2 46.9 - - + -
5087E ARG 4.0 3.1 - - - -
5088E THR* 1.3 76.4 - - - +
5090E LEU* 1.3 64.6 + - - +
5091E ARG 4.1 0.7 - - - -
5202E LEU* 4.2 12.0 - - + +
5206E CYS* 3.8 13.7 - - - -
5211E LEU* 3.8 20.6 - - + -
5212E ARG 2.5 17.4 + - - +
5213E ALA* 2.9 16.6 - - + +
5214E GLY 2.8 25.1 + - - +
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Residues in contact with LEU5090 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5021E LEU* 4.3 7.4 - - + -
5022E ALA 3.0 9.4 + - - +
5023E ILE* 3.2 8.7 - - + +
5024E VAL* 2.7 31.9 + - - +
5088E THR* 4.5 4.7 - - + -
5089E PHE* 1.3 82.2 - - - +
5091E ARG* 1.3 56.8 + - - +
5136E CYS* 3.7 22.2 - - + -
5140E LEU* 4.4 12.3 - - + -
5214E GLY* 3.7 8.3 - - - +
5245E VAL* 3.8 25.8 - - + +
5248E ALA* 4.4 5.2 - - + -
5249E ALA* 3.7 27.1 - - + +
5252E LEU* 3.6 34.3 - - + -
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Residues in contact with ARG5091 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5024E VAL* 3.4 19.2 + - + +
5025E PRO 3.9 1.0 - - - -
5026E GLY* 3.2 21.2 - - - +
5067E THR* 4.1 4.6 + - - +
5074E THR* 6.1 0.6 - - - +
5089E PHE 4.1 0.4 - - - -
5090E LEU* 1.3 74.6 - - - +
5092E ILE* 1.3 61.9 + - - +
5093E GLY* 4.1 7.7 - - - -
5094E THR 5.3 0.6 + - - -
5140E LEU* 5.6 0.3 - - - +
5196E GLU* 3.2 16.7 + - - +
5198E GLU* 3.2 44.6 + - - +
5199E SER 4.5 1.3 - - - +
5202E LEU* 3.5 27.1 - - + +
5214E GLY 3.0 9.9 + - - +
5215E MET* 3.2 32.1 - - + +
5216E VAL* 3.0 28.6 + - - +
5245E VAL* 5.0 0.6 - - - +
7005E SO4 3.0 33.8 + - - -
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Residues in contact with ILE5092 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5023E ILE* 4.0 10.1 - - + -
5024E VAL 3.7 2.2 + - - +
5025E PRO* 3.2 25.3 - - + +
5030E ARG* 3.4 21.0 + - - +
5034E ILE* 3.7 30.3 - - + -
5090E LEU 3.9 0.4 + - - -
5091E ARG* 1.3 77.4 - - - +
5093E GLY* 1.3 66.3 + - - +
5216E VAL* 3.3 16.2 - - + +
5238E GLU* 5.1 1.3 - - + +
5241E ALA* 3.8 26.7 - - + -
5242E VAL* 4.3 10.5 - - + +
5245E VAL* 3.8 29.2 - - + -
7005E SO4 4.0 0.7 + - - -
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Residues in contact with GLY5093 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5030E ARG* 3.6 17.7 - - - -
5091E ARG* 4.1 9.7 - - - +
5092E ILE* 1.3 79.6 - - - +
5094E THR* 1.3 59.2 - - - -
5216E VAL 3.1 10.3 + - - -
5217E ALA* 2.8 31.9 - - - +
5218E GLY 3.0 4.7 + - - -
7005E SO4 3.7 8.1 - - - -
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Residues in contact with THR5094 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2048C ARG* 4.8 3.5 + - - +
5030E ARG* 3.7 15.5 - - - +
5091E ARG* 5.3 0.9 + - - -
5093E GLY* 1.3 75.1 - - - -
5095E THR* 1.3 65.3 + - - +
5196E GLU* 4.4 9.0 - - - +
5217E ALA* 4.4 1.0 - - - +
5218E GLY 3.7 5.6 - - - -
5220E ILE* 4.1 26.1 - - + +
5234E MET* 5.5 7.6 - - + -
5238E GLU* 4.7 8.1 - - + +
7005E SO4 3.0 34.3 + - - +
8005E URA 4.2 15.2 + - - -
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Residues in contact with THR5095 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5094E THR* 1.3 80.0 - - - +
5096E GLY* 1.3 61.5 + - - +
5108E LEU* 3.9 15.7 - - + -
5194E ASN* 2.5 35.9 + - + +
5195E TYR 2.5 18.1 + - - -
5196E GLU* 4.6 2.0 - - - -
5217E ALA* 3.8 14.1 - - + -
5218E GLY 2.9 24.2 + - - +
5219E VAL* 3.2 9.1 - - + -
5220E ILE* 2.8 31.5 + - - +
8005E URA 3.8 13.8 - - - -
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Residues in contact with GLY5096 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5095E THR* 1.3 77.4 + - - +
5097E ALA* 1.3 67.1 + - - -
5098E ILE* 4.1 4.0 - - - +
5194E ASN* 3.9 2.7 - - - -
5195E TYR* 3.2 28.2 + - - +
5221E VAL* 3.0 26.5 - - - -
5223E ARG* 4.9 3.4 - - - +
8005E URA 3.5 13.3 - - - +
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Residues in contact with ALA5097 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5095E THR 4.1 0.2 - - - -
5096E GLY* 1.3 73.1 - - - +
5098E ILE* 1.3 60.5 + - - +
5099E GLN 4.3 0.2 - - - +
5102E ILE* 3.4 48.0 - - + +
5193E MET 3.6 8.1 - - - +
5194E ASN* 3.9 4.7 - - + +
5219E VAL* 3.9 17.8 - - + +
5221E VAL 3.0 5.5 + - - -
5222E ASN* 3.6 8.8 - - - +
5223E ARG* 3.2 24.9 + - - +
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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