Contacts of the strand formed by residues 5050 - 5057 (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 PHE5050 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2069C ILE* 4.3 18.4 - - + -
5008E HIS* 3.8 17.9 - + + -
5009E LEU* 3.4 38.8 - - + +
5045E ALA 3.7 2.6 - - - +
5046E SER* 3.4 2.3 - - - -
5047E HIS* 2.7 44.9 + - - +
5048E ARG* 3.1 7.9 + - + -
5049E GLU* 1.3 76.2 - - + +
5051E THR* 1.3 61.8 + - - +
5052E SER* 4.0 1.5 + - - -
5065E CYS* 4.7 2.2 - - - -
5066E SER* 3.4 18.2 - - - +
5067E THR* 3.8 4.7 - - - -
5073E SER* 3.2 46.7 - - - -
5076E ILE* 3.8 25.8 - - + -
5077E ALA* 4.0 9.2 - - + -
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Residues in contact with THR5051 (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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5028E PRO* 3.7 32.9 - - - +
5031E VAL* 3.4 10.8 - - + +
5032E GLU 5.9 0.2 - - - +
5043E LYS* 4.7 4.0 - - - -
5045E ALA 3.4 8.1 - - - +
5046E SER* 3.2 22.0 + - - +
5048E ARG 4.9 2.3 + - - -
5050E PHE* 1.3 71.6 + - - +
5052E SER* 1.3 60.3 + - - +
5053E TRP* 4.3 20.2 - - + +
5065E CYS* 3.5 1.8 - - - -
5066E SER* 2.9 35.4 + - - +
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Residues in contact with SER5052 (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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5009E LEU* 4.9 2.5 + - - -
5011E LEU* 3.6 23.6 - - - +
5043E LYS* 3.6 1.2 - - - +
5044E LEU* 3.0 30.1 + - - +
5045E ALA* 2.8 36.0 + - - +
5050E PHE 4.0 1.2 + - - -
5051E THR* 1.3 73.2 - - - +
5053E TRP* 1.3 73.5 + - - +
5063E ILE* 5.1 2.9 - - - -
5064E VAL 3.3 7.2 - - - -
5065E CYS* 4.1 17.0 - - - +
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Residues in contact with TRP5053 (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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5031E VAL* 3.7 24.0 - - + -
5032E GLU* 3.7 50.1 - - + +
5035E ALA* 3.7 25.4 - - + -
5036E ALA* 5.8 0.4 - - - -
5041E PRO* 4.0 13.2 - - + -
5042E VAL* 3.2 43.1 - - - -
5043E LYS* 3.5 31.7 - - + +
5044E LEU* 3.9 6.3 - - - +
5051E THR* 4.3 9.7 - - + +
5052E SER* 1.3 91.0 - - - +
5054E ARG* 1.3 60.3 + - - +
5063E ILE* 3.5 6.4 - - - +
5064E VAL* 2.9 30.8 + - + +
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Residues in contact with ARG5054 (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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5015E ASP* 2.8 29.1 + - - +
5016E LEU 3.5 10.1 - - - +
5017E GLN* 3.0 45.3 + - - +
5040E LYS 4.0 3.9 + - - +
5041E PRO* 3.4 1.2 - - - +
5042E VAL* 2.8 51.0 + - - +
5044E LEU* 3.2 35.7 - - + +
5053E TRP* 1.3 77.2 - - - +
5055E ALA* 1.3 69.8 + - - +
5061E ALA* 4.3 7.8 - - + +
5062E VAL 3.3 13.0 - - - +
5063E ILE* 3.6 8.1 - - + -
5064E VAL* 6.1 0.2 - - - -
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Residues in contact with ALA5055 (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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5035E ALA* 4.3 2.7 - - + +
5038E MET* 3.4 37.0 - - + -
5039E ASP 3.5 12.8 - - - +
5040E LYS 4.0 4.0 - - - -
5041E PRO* 3.8 14.1 - - + -
5054E ARG* 1.3 80.3 + - - +
5056E GLU* 1.3 62.5 + - - +
5061E ALA* 3.3 8.0 - - - +
5062E VAL* 2.8 29.2 + - - +
5064E VAL* 5.8 0.2 - - + -
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Residues in contact with GLU5056 (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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5017E GLN* 5.9 1.0 + - - -
5038E MET* 3.4 7.6 - - - +
5039E ASP* 2.7 52.4 + - + +
5040E LYS* 3.4 36.8 - - + +
5055E ALA* 1.3 74.9 - - - +
5057E LEU* 1.3 67.6 + - - +
5059E GLY* 3.6 29.4 + - - +
5060E LYS 3.4 14.4 - - - +
5061E ALA* 4.4 3.6 - - + +
5062E VAL* 4.5 0.4 - - - +
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Residues in contact with LEU5057 (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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5037E LEU 5.0 0.4 - - - +
5038E MET* 3.8 34.8 - - + -
5039E ASP* 4.6 7.4 - - - +
5056E GLU* 1.3 82.5 - - - +
5058E ASP* 1.3 62.4 + - - +
5059E GLY 2.9 3.4 - - - +
5060E LYS* 2.7 37.5 + - - +
5062E VAL* 4.3 6.1 - - + -
5246E VAL* 3.9 24.7 - - + +
5249E ALA* 4.6 4.9 - - + -
5250E ARG* 3.1 57.0 - - + +
5253E LEU* 3.3 15.6 - - + +
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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