Contacts of the strand formed by residues 118 - 122 (chain B) in PDB entry 1U5U
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 SER 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B HIS* 3.4 14.3 - - - -
102B ARG 4.3 2.6 + - - -
103B HIS* 2.7 40.3 - - - +
104B ALA* 2.8 33.4 + - - +
117B ARG* 1.3 72.5 - - - +
119B PHE* 1.3 53.2 + - - +
136B MET 3.2 14.6 - - - -
137B ASN* 3.4 13.2 - - - -
187B PHE* 4.5 0.2 - - - -
192B TYR* 3.3 8.0 - - - -
999B HEM 3.5 16.3 + - - +
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Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.4 21.3 - - + -
102B ARG 3.8 3.1 - - - -
103B HIS* 3.7 18.2 - - - -
118B SER* 1.3 71.7 - - - +
120B SER* 1.3 62.6 + - - +
121B ILE* 3.4 38.4 - - + -
134B ILE 3.9 0.2 - - - +
136B MET* 2.8 60.6 + - + +
192B TYR* 3.1 37.4 - + + -
214B ALA* 3.7 12.1 - - + -
269B TYR* 3.5 28.3 - + + -
271B LEU* 4.9 0.7 - - + -
306B VAL* 4.6 7.6 - - + -
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Residues in contact with SER 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LEU* 3.3 5.6 - - - +
102B ARG 2.9 37.6 + - - -
118B SER* 4.8 0.3 - - - -
119B PHE* 1.3 72.0 - - - +
121B ILE* 1.3 62.4 + - - +
134B ILE 3.3 7.4 - - - -
135B VAL* 3.3 9.3 - - - +
322B PHE* 3.4 27.3 - - - -
999B HEM 3.0 42.3 + - - +
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Residues in contact with ILE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.2 13.7 - - + -
99B ALA* 5.7 1.1 - - + -
100B ARG 3.3 4.7 - - - +
101B LEU* 3.9 18.6 - - + -
119B PHE* 3.4 40.2 - - + -
120B SER* 1.3 78.0 - - - +
122B LYS* 1.3 60.4 - - - +
123B PHE* 3.8 22.1 + - + -
132B LEU 4.0 0.5 - - - +
133B ASP* 3.2 6.6 - - - +
134B ILE* 2.9 48.9 + - + +
271B LEU* 4.2 19.5 - - + -
306B VAL* 4.6 11.0 - - + -
308B ILE* 5.7 0.2 - - + -
322B PHE* 3.7 4.4 - - - -
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Residues in contact with LYS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.6 0.2 - - - -
99B ALA* 3.1 23.6 - - - +
100B ARG* 2.9 12.3 + - + +
121B ILE* 1.3 73.2 - - - +
123B PHE* 1.3 62.5 + - - +
124B ALA* 2.9 25.9 + - + +
126B SER* 3.5 33.7 - - - +
127B ASP 3.9 8.3 - - - -
128B SER 4.2 1.6 - - - -
129B ASP 2.9 28.4 + - - +
130B GLY* 4.9 0.9 - - - -
132B LEU 4.5 0.7 - - - +
133B ASP* 2.8 36.1 + - - +
320B THR* 4.0 9.9 - - + -
321B ALA 2.8 29.6 + - - -
322B PHE* 3.9 9.6 - - + -
326B ASN* 3.8 1.6 - - - +
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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
------------------------------------------------------------
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