Contacts of the strand formed by residues 141 - 145 (chain G) in PDB entry 5JLH
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 PHE 141 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G TYR* 3.4 10.6 - - - +
138G SER* 2.8 36.4 + - - +
139G GLY* 5.6 0.2 - - - -
140G LEU* 1.3 82.9 - - - +
142G CYS* 1.3 59.5 + - - +
143G VAL* 4.0 11.4 - - + -
503G GLN* 4.2 1.6 - - - -
506G PHE* 3.2 45.1 - + - -
692G PHE* 3.9 11.7 - - + -
694G ARG* 3.1 61.2 - - + -
719G ASN 4.2 0.2 - - - -
720G GLY 3.9 15.5 - - - -
721G VAL* 3.7 28.3 - - + -
724G GLY* 4.2 7.4 - - - -
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Residues in contact with CYS 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135G TYR* 4.4 21.5 - - - -
136G THR 3.8 5.4 - - - -
137G TYR* 4.0 20.2 - - + -
140G LEU 5.2 0.2 - - - +
141G PHE* 1.3 73.7 - - - +
143G VAL* 1.3 62.7 + - - +
173G HIS 4.1 12.6 - - - -
174G VAL* 4.9 1.8 - - - -
177G VAL* 3.7 27.4 - - + -
692G PHE 3.2 17.3 + - - +
693G VAL* 3.4 15.7 - - + +
694G ARG 2.8 25.2 + - - -
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Residues in contact with VAL 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G MET* 5.3 0.4 - - - -
125G LEU* 4.3 26.5 - - + -
134G ILE 3.4 2.0 - - - +
135G TYR* 3.4 5.0 - - - -
136G THR* 2.6 49.9 + - - +
138G SER* 4.1 25.4 - - - +
141G PHE* 4.3 9.9 - - + -
142G CYS* 1.3 74.7 - - - +
144G VAL* 1.3 66.1 + - - +
145G ILE* 4.4 6.1 - - + -
694G ARG* 3.4 10.5 - - + -
696G ILE* 3.7 25.6 - - + -
716G LEU* 5.7 0.9 - - + -
721G VAL* 4.7 9.6 - - + -
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134G ILE* 3.2 36.6 - - + -
135G TYR* 3.4 25.1 - - + -
142G CYS* 5.6 0.2 - - - -
143G VAL* 1.3 72.9 - - - +
145G ILE* 1.3 66.1 + - - +
146G ASN* 4.2 2.2 + - - +
207G ASN* 4.1 15.0 - - - +
693G VAL* 4.1 13.0 - - + -
694G ARG 2.8 17.4 + - - +
695G CYS* 3.7 24.2 - - + -
696G ILE* 3.0 25.5 + - - +
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Residues in contact with ILE 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G LEU* 4.3 38.4 - - + +
129G TYR* 4.0 26.7 - - + -
134G ILE* 3.1 24.5 + - - +
143G VAL* 4.4 8.3 - - + -
144G VAL* 1.3 80.0 - - - +
146G ASN* 1.3 64.6 + - - +
147G PRO* 3.1 10.2 - - - +
696G ILE* 3.3 32.1 - - + +
698G PRO* 3.7 22.4 - - + -
707G LEU* 4.5 16.4 - - + -
712G VAL* 5.5 2.5 - - + -
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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