Contacts of the strand formed by residues 149 - 153 (chain G) in PDB entry 4UJ3
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 149 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118G VAL* 4.6 4.3 - - - +
119G ILE 3.4 12.0 + - - -
120G MET* 3.6 23.3 - - - +
121G LEU* 3.0 21.1 + - - +
148G LEU* 1.3 80.1 - - - +
150G PHE* 1.3 61.7 + - - +
167G THR* 4.8 3.8 - - - -
171G GLU* 2.8 36.2 + - - -
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Residues in contact with PHE 150 (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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91G TYR* 3.5 14.8 - + - -
120G MET* 4.5 1.6 - - - -
121G LEU* 3.4 24.2 - - + -
136G THR* 3.8 15.3 - - + -
139G ALA* 3.3 39.3 - - + -
140G ARG* 3.6 45.1 - - + +
143G ALA* 3.6 14.8 - - + -
144G GLU* 6.3 0.7 - - + -
148G LEU 4.7 0.4 - - - +
149G SER* 1.3 78.8 - - - +
151G ILE* 1.3 77.7 + - - +
152G GLU* 3.9 25.1 - - + -
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Residues in contact with ILE 151 (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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120G MET* 3.6 34.1 - - + -
121G LEU 3.0 10.7 + - - +
122G VAL* 3.4 9.0 - - + +
123G GLY* 3.2 19.2 - - - -
150G PHE* 1.3 82.8 - - - +
152G GLU* 1.3 73.8 + - - +
153G THR* 4.2 2.0 - - + -
160G ASN* 3.3 49.8 - - + +
163G ALA* 4.2 7.4 - - + -
164G ALA* 3.9 17.5 - - + +
167G THR* 5.5 3.1 - - - +
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Residues in contact with GLU 152 (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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91G TYR* 4.4 5.5 + - - +
93G ILE* 4.6 7.0 - - - +
123G GLY* 2.9 12.3 - - - +
126G SER* 4.4 13.3 + - - -
132G ARG* 3.0 34.7 + - - -
134G VAL 4.5 0.7 - - - +
136G THR* 2.9 37.2 + - + +
150G PHE* 3.9 17.7 - - + -
151G ILE* 1.3 77.9 - - - +
153G THR* 1.3 63.5 + - - +
159G THR* 4.6 3.8 - - - +
160G ASN* 2.9 30.4 + - - +
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Residues in contact with THR 153 (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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27G LEU* 3.7 13.1 - - + +
122G VAL* 3.1 28.5 - - + +
123G GLY 2.4 19.0 + - - -
124G ASN* 2.6 33.2 + - - +
125G LYS 2.9 15.1 + - - -
126G SER* 3.2 11.1 + - - -
151G ILE* 4.2 4.0 - - + -
152G GLU* 1.3 76.3 - - - +
154G SER* 1.3 60.7 + - - +
159G THR 3.3 9.0 - - - -
160G ASN* 3.7 24.7 - - + +
161G VAL* 4.3 2.0 - - - +
164G ALA* 3.9 13.9 - - + -
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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