Contacts of the strand formed by residues 133 - 138 (chain R) in PDB entry 5FYW
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 TYR 133 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118Q LEU* 3.4 1.7 - - - -
119Q LEU* 2.6 55.8 + - + +
121Q PHE* 4.8 11.9 - + - -
127Q ILE 3.7 7.3 + - - -
128Q ASN 3.3 21.2 + - - -
129Q PRO* 3.2 30.3 - - + +
130Q VAL* 3.9 24.5 - - + -
64R SER* 6.0 4.5 - - - -
129R VAL 6.0 0.2 - - - -
130R GLU* 5.6 3.4 - - - -
131R ASN 4.1 8.5 + - - -
132R GLU* 1.3 95.4 - - - +
134R VAL* 1.3 64.3 + - - +
214R ILE* 5.5 6.5 - - + -
216R GLY 3.6 7.9 - - - +
217R THR* 3.3 40.3 - - + +
218R VAL* 4.0 4.2 - - - +
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Residues in contact with VAL 134 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q THR* 3.3 30.5 - - + -
117Q HIS 3.7 6.3 - - - +
118Q LEU* 3.8 15.5 - - + -
119Q LEU* 4.6 0.9 - - - -
375Q LEU* 3.6 14.1 - - + -
68R VAL* 3.6 30.3 - - + -
133R TYR* 1.3 79.7 - - - +
135R PHE* 1.3 66.2 + - - +
214R ILE* 4.0 4.3 - - - +
215R VAL* 2.9 34.7 + - + +
216R GLY 2.9 13.5 + - - +
218R VAL* 3.8 10.3 - - + -
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Residues in contact with PHE 135 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116Q THR* 3.2 10.9 - - - +
117Q HIS* 2.9 78.5 + + + -
118Q LEU 4.0 0.7 - - - -
119Q LEU* 3.3 38.1 - - + -
139Q LEU* 4.0 25.4 - - + -
350Q TRP* 3.7 32.1 - + - -
393Q TYR* 5.2 0.7 - + - -
395Q PHE* 4.9 1.8 - + - -
134R VAL* 1.3 75.5 - - - +
136R THR* 1.3 89.8 + - - +
137R GLU* 5.2 4.3 - - + -
213R ALA 3.5 11.4 - - - +
214R ILE* 4.2 14.8 - - + -
215R VAL* 3.6 8.5 - - - +
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Residues in contact with THR 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114Q MET* 3.7 33.0 - - + +
115Q ARG 3.0 9.4 - - - +
116Q THR* 3.4 20.9 - - + +
135R PHE* 1.3 98.5 - - - +
137R GLU* 1.3 62.4 + - - +
212R THR* 4.4 2.3 - - - +
213R ALA* 3.2 34.1 + - - +
214R ILE 4.9 0.3 + - - -
215R VAL* 3.5 20.7 - - + +
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Residues in contact with GLU 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113Q ASN 3.7 0.3 - - - +
114Q MET* 3.1 30.5 - - - +
115Q ARG* 3.1 14.3 + - + +
117Q HIS* 4.8 13.1 - - + -
141Q ARG* 5.4 0.5 - - - -
350Q TRP* 4.6 17.8 - - - -
135R PHE* 5.2 4.0 - - + -
136R THR* 1.3 77.1 - - - +
138R GLN* 1.3 81.9 + - - +
210R LYS* 3.1 36.6 - - + +
211R LYS 3.2 15.3 - - - +
212R THR* 5.0 2.5 - - - +
213R ALA 5.3 0.2 - - - +
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Residues in contact with GLN 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113Q ASN* 4.0 14.8 - - + +
114Q MET* 3.3 34.9 - - + +
62R GLU* 5.7 1.0 + - - -
136R THR* 6.0 0.2 - - - +
137R GLU* 1.3 88.9 - - - +
210R LYS* 5.1 1.6 - - - +
211R LYS* 2.9 56.2 + - + +
212R THR* 4.7 3.0 + - - +
213R ALA* 5.4 9.5 - - + +
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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
------------------------------------------------------------
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