Contacts of the strand formed by residues 4088 - 4097 (chain F) 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 THR4088 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4020F GLN 3.2 8.0 + - - -
4021F LEU* 3.3 23.6 - - + +
4022F ALA 2.8 26.3 + - - -
4086F ILE* 3.4 3.9 - - - +
4087F ARG* 1.3 81.8 - - - +
4089F PHE* 1.3 67.2 + - - +
4090F LEU* 4.9 0.9 - - + -
4136F CYS* 3.8 24.0 - - - -
4212F ARG* 3.1 42.2 + - - +
4252F LEU* 4.7 5.6 + - + -
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Residues in contact with PHE4089 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022F ALA* 3.2 6.5 - - + +
4024F VAL* 4.4 19.1 - - + -
4078F VAL* 3.9 35.4 - - + -
4081F LEU* 3.8 19.7 - - + -
4082F ALA* 4.2 3.6 - - + -
4086F ILE* 3.3 46.9 - - + -
4087F ARG 4.1 2.9 - - - -
4088F THR* 1.3 78.5 - - - +
4090F LEU* 1.3 63.3 + - - +
4091F ARG 4.0 0.8 + - - -
4202F LEU* 4.2 17.9 - - + +
4206F CYS* 3.9 12.1 - - - -
4211F LEU* 4.0 19.1 - - + -
4212F ARG 2.7 18.8 + - - +
4213F ALA* 3.0 5.1 - - + +
4214F GLY 3.0 24.9 + - - +
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Residues in contact with LEU4090 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4021F LEU* 4.5 9.9 - - + -
4022F ALA 2.8 12.7 + - - +
4023F ILE* 3.2 10.9 - - + +
4024F VAL* 2.9 24.5 + - - -
4088F THR* 4.9 1.6 - - + -
4089F PHE* 1.3 80.4 - - - +
4091F ARG* 1.3 61.5 + - - +
4136F CYS* 4.0 11.9 - - + -
4140F LEU* 4.4 13.0 - - + -
4214F GLY* 3.8 16.8 - - - +
4245F VAL* 3.8 22.4 - - + +
4248F ALA* 4.0 5.4 - - + -
4249F ALA* 3.7 30.1 - - + +
4252F LEU* 3.6 32.8 - - + -
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Residues in contact with ARG4091 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4024F VAL* 3.7 17.2 + - + +
4026F GLY* 3.9 8.7 - - - +
4067F THR* 5.5 1.2 + - - -
4074F THR* 6.1 0.9 - - - -
4089F PHE 4.0 1.2 - - - -
4090F LEU* 1.3 72.9 - - - +
4092F ILE* 1.3 67.1 + - - +
4093F GLY* 3.7 10.1 - - - -
4094F THR 4.4 1.0 + - - +
4140F LEU* 5.6 0.2 - - - +
4196F GLU* 2.7 36.2 + - - +
4197F MET 4.7 0.4 - - - +
4198F GLU* 3.0 34.4 + - - +
4199F SER 4.4 1.6 - - - +
4202F LEU* 3.5 27.6 - - + +
4214F GLY 3.1 9.6 + - - +
4215F MET* 3.3 23.9 - - - +
4216F VAL* 3.2 31.1 + - - +
4245F VAL* 4.9 0.4 - - - -
7004F SO4 2.9 40.2 + - - -
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Residues in contact with ILE4092 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4023F ILE* 4.1 9.4 - - + -
4024F VAL 3.7 1.4 + - - -
4025F PRO* 3.3 42.2 - - + +
4034F ILE* 3.9 15.5 - - + -
4091F ARG* 1.3 80.0 + - - +
4093F GLY* 1.3 64.7 + - - +
4216F VAL* 3.4 14.6 - - + +
4238F GLU* 6.3 0.7 - - + -
4241F ALA* 3.1 47.8 - - + +
4242F VAL* 4.3 13.2 - - + -
4245F VAL* 4.1 16.8 - - + -
7004F SO4 3.7 2.6 + - - -
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Residues in contact with GLY4093 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4091F ARG* 3.6 11.4 - - - +
4092F ILE* 1.3 80.5 - - - +
4094F THR* 1.3 66.5 + - - +
4216F VAL 3.1 10.7 + - - -
4217F ALA* 3.1 7.2 - - - -
4218F GLY 3.1 20.1 + - - -
4241F ALA* 4.9 0.9 - - - +
7004F SO4 3.3 17.5 - - - -
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Residues in contact with THR4094 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1048A ARG* 4.4 6.0 + - - +
4091F ARG* 4.6 0.3 + - - -
4093F GLY* 1.3 76.9 - - - +
4095F THR* 1.3 64.2 + - - +
4196F GLU* 4.4 6.4 - - - +
4217F ALA* 4.3 0.7 - - - -
4218F GLY* 3.5 7.9 - - - +
4220F ILE* 4.1 27.3 - - + +
4234F MET* 4.4 19.1 - - + +
4237F THR* 6.3 0.9 - - + -
4238F GLU* 5.6 10.8 - - + +
7004F SO4 2.7 31.8 + - - +
8004F URA 3.3 22.0 + - - -
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Residues in contact with THR4095 (chain F).
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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4094F THR* 1.3 77.7 - - - +
4096F GLY* 1.3 60.7 + - - +
4097F ALA 4.2 0.2 - - - -
4108F LEU* 3.8 19.1 - - + -
4194F ASN* 2.9 33.6 + - + +
4195F TYR 2.5 21.8 + - - -
4196F GLU* 4.3 3.6 - - - -
4217F ALA* 3.9 18.2 - - + +
4218F GLY 3.1 11.1 + - - +
4219F VAL* 3.6 8.7 - - + +
4220F ILE* 2.9 31.5 + - - +
8004F URA 3.6 11.4 - - - -
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Residues in contact with GLY4096 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4095F THR* 1.3 81.4 + - - +
4097F ALA* 1.3 66.2 + - - -
4098F ILE* 3.5 2.1 + - - +
4194F ASN* 3.3 2.2 - - - -
4195F TYR* 3.0 32.3 + - - +
4221F VAL* 3.3 21.8 - - - -
4223F ARG* 4.6 6.0 - - - +
8004F URA 3.8 9.9 - - - -
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Residues in contact with ALA4097 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4095F THR 4.2 0.2 - - - -
4096F GLY* 1.3 71.8 - - - +
4098F ILE* 1.3 61.2 + - - +
4099F GLN 4.3 1.1 - - - +
4102F ILE* 3.5 49.1 - - + +
4193F MET 3.3 7.0 - - - +
4194F ASN* 4.3 3.1 - - - +
4219F VAL* 3.8 13.9 - - + +
4221F VAL 2.9 7.8 + - - +
4222F ASN* 3.6 8.2 - - - +
4223F ARG* 2.9 28.8 + - - +
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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