Contacts of the strand formed by residues 141 - 148 (chain G) in PDB entry 5KZ5
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 GLY 141 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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872 ASN* 3.9 9.4 - - - +
136G LEU* 3.6 24.4 - - - +
139G ASP 3.4 1.9 + - - -
140G LEU* 1.3 83.2 + - - +
142G THR* 1.4 69.0 + - - +
143G TYR* 3.4 17.0 - - - -
159G PRO* 4.1 9.9 - - - -
96J GLU* 5.1 0.2 - - - -
162L GLY* 4.9 3.1 - - - -
163L PRO* 5.3 1.3 - - - -
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Residues in contact with THR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 ASN* 4.0 5.2 - - - +
134G VAL* 3.4 23.9 - - + +
135G LYS 3.3 26.7 - - - +
136G LEU* 3.9 20.6 - - + +
141G GLY* 1.4 79.1 - - - +
143G TYR* 1.4 65.6 + - - +
144G VAL* 4.3 7.8 - - - +
157G SER* 3.8 11.3 + - - +
159G PRO* 3.5 20.7 - - - +
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Residues in contact with TYR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 ASN* 3.8 9.9 - - + +
892 HIS 3.6 13.0 - - - +
902 SER* 3.6 26.0 - - - +
952 TYR* 5.5 4.8 + + - -
132G LEU* 4.2 0.2 - - - +
134G VAL* 3.4 18.5 - - - +
140G LEU* 4.0 20.7 - - + +
141G GLY 3.4 31.0 - - - -
142G THR* 1.4 60.5 + - - -
144G VAL* 1.4 64.8 + - - +
145G ILE* 5.0 2.5 - - + -
156G LEU* 6.5 0.4 - - + -
157G SER 2.9 16.5 + - - -
158G SER* 4.8 1.6 - - - -
159G PRO* 3.5 29.0 - - + +
160G SER* 5.2 2.3 - - - -
186G LEU* 5.0 14.1 - - + -
189G GLU* 3.9 33.8 + - - +
190G LEU* 4.8 14.9 - - + +
133g PRO* 5.1 7.3 - - - +
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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
----------------------------------------------------------
132G LEU* 3.7 36.6 - - + +
134G VAL* 3.9 24.5 - - + -
142G THR* 4.3 7.6 - - - +
143G TYR* 1.4 81.1 - - - +
145G ILE* 1.4 80.5 + - - +
146G ASN* 3.8 19.5 - - + +
155G TRP* 5.9 0.9 - - + -
156G LEU* 3.7 8.1 - - - +
157G SER* 3.5 37.6 + - - +
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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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892 HIS 4.8 4.5 - - - +
902 SER* 5.6 0.4 - - - -
103G LEU* 3.7 21.9 - - + +
106G LEU* 4.0 17.3 - - + -
110G PHE* 4.4 5.8 - - + -
130G GLY 3.6 5.9 - - - +
132G LEU* 3.2 40.5 + - + +
143G TYR* 5.0 0.9 - - + -
144G VAL* 1.4 87.4 - - - +
146G ASN* 1.4 60.7 + - - +
154G ILE* 3.7 18.6 - - + -
155G TRP 4.0 4.3 - - - +
156G LEU* 4.1 5.4 - - + +
173G TRP* 4.7 1.6 - - + -
182G LEU* 3.9 30.7 - - + -
186G LEU* 3.9 23.3 - - + -
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Residues in contact with ASN 146 (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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103G LEU* 4.7 0.7 - - - -
130G GLY 3.6 3.4 - - - -
131G VAL* 4.0 22.9 - - + -
132G LEU 4.4 1.8 - - - +
144G VAL* 3.8 19.6 - - + +
145G ILE* 1.4 74.6 + - - +
147G LYS* 1.4 72.6 + - - +
148G GLN* 4.1 10.3 + - - -
154G ILE* 3.6 9.9 - - - +
155G TRP* 3.1 74.5 + - - +
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Residues in contact with LYS 147 (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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100G GLU* 4.2 33.7 + - + +
103G LEU* 3.9 18.2 - - + +
129G SER* 3.4 31.9 + - - +
130G GLY 3.1 17.4 + - - +
131G VAL* 4.3 6.2 - - + +
146G ASN* 1.4 82.8 + - - +
148G GLN* 1.4 65.2 + - - +
149G THR* 3.9 25.5 - - - +
152G LYS* 5.7 5.4 - - - +
153G GLN 4.1 5.6 - - - +
154G ILE* 4.4 2.0 - - + -
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Residues in contact with GLN 148 (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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146G ASN* 4.1 17.8 + - - +
147G LYS* 1.4 75.9 - - - +
149G THR* 1.4 86.2 + - - +
151G ASN* 3.4 20.7 + - - +
152G LYS* 3.1 21.5 + - - -
153G GLN* 3.1 32.3 + - + +
154G ILE 4.8 0.4 - - - +
155G TRP* 4.8 11.9 - - + +
150H PRO* 5.1 8.2 - - + +
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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