Contacts of the strand formed by residues 130 - 137 (chain G) in PDB entry 5LK5
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 ILE 130 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 3.9 17.7 - - + -
93G VAL* 5.8 1.1 - - + -
111G LYS* 3.4 2.8 - - - -
112G LEU* 2.8 46.5 + - + +
128G TYR* 3.6 6.2 - - - -
129G ASN* 1.3 86.8 - - + +
131G MET* 1.3 72.8 + - - +
132G PHE* 4.6 2.0 - - + +
146G VAL* 5.5 0.4 - - + -
147G ILE 3.3 10.8 - - - +
148G PHE* 3.9 26.7 - - + -
174G LEU* 4.1 22.0 - - + -
176G VAL* 5.1 4.3 - - + -
306G TYR 5.3 1.6 - - - +
308G TYR* 3.9 12.6 - - + -
311G PHE* 3.9 24.2 - - + -
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Residues in contact with MET 131 (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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109G TYR* 3.6 39.3 - - + -
110G VAL 3.4 13.0 - - - +
111G LYS* 4.1 20.4 - - + +
128G TYR* 3.8 19.7 - - + -
130G ILE* 1.3 77.6 - - - +
132G PHE* 1.3 65.6 + - - +
145G HIS* 3.5 40.6 - - + +
146G VAL* 3.5 4.2 - - - -
147G ILE* 2.9 54.1 + - + +
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Residues in contact with PHE 132 (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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93G VAL* 4.0 12.8 - - + -
95G PHE* 3.6 15.8 - + - -
109G TYR* 3.4 4.9 - - - -
110G VAL* 2.9 38.5 + - + +
112G LEU* 6.5 0.4 - - + -
130G ILE* 4.7 3.1 - - + -
131G MET* 1.3 77.3 - - - +
133G GLY* 1.3 61.3 + - - +
144G VAL* 3.8 20.9 - - + -
145G HIS 3.3 10.3 - - - -
146G VAL* 4.0 11.0 - - + -
172G TYR* 3.9 20.4 - + + -
173G THR 3.5 33.4 - - - -
174G LEU* 3.5 45.1 - - + -
184G VAL* 4.0 14.4 - - + -
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Residues in contact with GLY 133 (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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95G PHE* 4.2 3.8 - - - -
109G TYR* 3.6 9.4 - - - +
132G PHE* 1.3 82.9 - - - +
134G PRO* 1.3 76.7 - - - +
135G ASP 3.7 0.2 + - - -
144G VAL* 4.0 9.4 - - - -
145G HIS* 2.9 37.0 + - - +
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Residues in contact with PRO 134 (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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95G PHE* 4.4 1.8 - - + -
97G VAL* 4.2 9.6 - - + -
99G HIS* 4.7 10.1 - - - +
108G GLY* 2.8 55.4 + - - +
109G TYR* 3.5 4.7 - - - -
133G GLY* 1.3 87.0 - - - +
135G ASP* 1.3 54.9 + - - +
136G ILE* 5.2 1.1 - - + -
143G LYS 3.4 7.2 - - - +
144G VAL* 4.4 1.8 - - + -
163G CYS* 3.8 15.3 - - + -
164G LYS 5.2 0.7 - - - +
172G TYR* 3.7 50.7 - - + +
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Residues in contact with ASP 135 (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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106G GLY 3.6 5.5 - - - +
107G GLY* 3.5 16.3 + - - -
109G TYR* 3.9 12.9 + - + -
134G PRO* 1.3 76.1 - - - +
136G ILE* 1.3 74.9 + - - +
137G CYS* 5.4 2.3 - - - +
141G THR* 3.7 13.6 - - + +
143G LYS* 2.8 36.6 + - + +
145G HIS* 3.1 37.3 + - + +
163G CYS* 4.4 0.2 - - - -
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Residues in contact with ILE 136 (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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99G HIS* 4.0 15.0 - - + +
103G ILE* 3.8 33.9 - - + +
104G ASP 3.8 14.8 - - - +
105G CYS* 3.8 0.3 - - - -
106G GLY* 2.7 41.0 + - - +
134G PRO 5.2 0.4 - - - -
135G ASP* 1.3 86.8 + - - +
137G CYS* 1.3 65.1 + - - +
138G GLY 4.4 3.4 - - - +
141G THR* 3.3 10.3 - - - +
142G LYS* 4.2 11.4 - - + -
163G CYS* 3.8 12.3 - - - -
164G LYS 3.6 24.2 - - - +
165G ASP* 4.1 15.3 - - + +
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Residues in contact with CYS 137 (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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104G ASP 3.7 2.5 - - - -
105G CYS* 2.2 40.4 - - - -
135G ASP* 5.4 2.5 - - - +
136G ILE* 1.3 75.5 - - - +
138G GLY* 1.3 65.8 + - - +
140G GLY* 4.2 1.2 + - - -
141G THR* 3.0 35.6 + - + +
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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
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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