Contacts of the strand formed by residues 130 - 137 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91H LEU* 4.6 8.7 - - + -
93H VAL* 5.7 0.9 - - + -
110H VAL 4.2 0.2 - - - +
111H LYS* 3.4 2.6 - - - -
112H LEU* 2.8 48.1 + - + +
128H TYR* 3.7 5.7 - - - -
129H ASN* 1.3 78.3 - - - +
131H MET* 1.3 71.4 + - - +
132H PHE* 4.6 2.2 - - + +
146H VAL* 5.5 0.2 - - + -
147H ILE 3.3 12.6 - - - +
148H PHE* 3.3 28.5 - - + -
174H LEU* 4.1 25.1 - - + -
176H VAL* 5.7 0.9 - - + -
306H TYR 5.1 0.7 - - - +
308H TYR* 3.1 37.5 - - + -
311H PHE* 4.1 18.6 - - + -
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Residues in contact with MET 131 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109H TYR* 3.6 39.5 - - + +
110H VAL 3.4 12.1 - - - +
111H LYS* 4.1 20.0 - - + -
128H TYR* 3.8 19.7 - - + -
130H ILE* 1.3 75.0 - - - +
132H PHE* 1.3 64.6 - - - +
145H HIS* 3.5 40.2 - - + +
146H VAL* 3.5 3.3 - - - -
147H ILE* 2.8 57.5 + - + +
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Residues in contact with PHE 132 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93H VAL* 3.9 13.2 - - + -
95H PHE* 3.6 17.1 - + - -
109H TYR* 3.4 5.1 - - - -
110H VAL* 2.9 38.7 + - + +
130H ILE* 4.5 2.9 + - + +
131H MET* 1.3 76.2 - - - +
133H GLY* 1.3 63.2 + - - +
144H VAL* 3.8 21.3 - - + -
145H HIS 3.3 10.1 - - - -
146H VAL* 4.0 10.3 - - + -
172H TYR* 3.9 19.7 - + + -
173H THR 3.5 33.0 - - - -
174H LEU* 3.5 46.2 - - + -
184H VAL* 4.1 14.4 - - + -
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Residues in contact with GLY 133 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PHE* 4.2 4.3 - - - -
109H TYR* 3.6 9.5 - - - +
132H PHE* 1.3 80.9 - - - +
134H PRO* 1.3 76.7 - - - +
135H ASP 3.7 0.2 + - - -
144H VAL* 3.9 11.0 - - - -
145H HIS* 2.9 38.0 + - - +
172H TYR* 5.1 0.2 - - - -
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Residues in contact with PRO 134 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H PHE* 4.5 1.8 - - + -
97H VAL* 4.2 10.8 - - + -
99H HIS* 4.7 9.2 - - + +
106H GLY 5.2 0.2 - - - -
108H GLY* 2.8 54.1 + - - +
109H TYR* 3.5 4.5 - - - -
133H GLY* 1.3 85.3 - - - +
135H ASP* 1.3 56.5 + - - +
136H ILE* 5.2 0.9 - - + -
143H LYS 3.4 7.6 - - - +
144H VAL* 4.4 1.1 - - + -
163H CYS* 3.8 15.9 - - + -
164H LYS 5.2 0.7 - - - +
172H TYR* 3.7 50.7 - - + +
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Residues in contact with ASP 135 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H GLY* 3.5 4.9 - - - +
107H GLY* 3.5 16.6 + - - -
109H TYR* 3.9 13.5 + - + -
134H PRO* 1.3 74.9 - - - +
136H ILE* 1.3 74.9 + - - +
137H CYS* 5.4 2.2 - - - +
141H THR* 3.7 13.4 - - + +
142H LYS* 3.7 1.7 - - - -
143H LYS* 2.8 37.1 + - + +
145H HIS* 3.1 37.1 + - + +
163H CYS* 4.4 0.2 - - - -
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Residues in contact with ILE 136 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99H HIS* 4.0 13.9 - - + +
103H ILE* 3.8 35.9 - - + +
104H ASP 3.8 13.9 - - - +
105H CYS* 3.8 0.6 - - - -
106H GLY 2.7 41.4 + - - +
134H PRO 5.2 0.4 - - - -
135H ASP* 1.3 84.8 + - - +
137H CYS* 1.3 66.7 + - - +
138H GLY 4.5 5.2 - - - +
141H THR* 3.3 11.2 - - - +
142H LYS* 4.9 6.5 - - + +
163H CYS* 3.8 12.3 - - - -
164H LYS 3.6 23.8 - - - +
165H ASP* 4.0 16.8 - - + -
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Residues in contact with CYS 137 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ASP 3.7 2.2 - - - -
105H CYS* 2.1 40.6 - - - -
135H ASP* 5.4 3.1 - - - +
136H ILE* 1.3 74.1 - - - +
138H GLY* 1.3 66.9 + - - +
139H PRO* 4.4 0.7 - - - +
140H GLY* 4.2 1.4 + - - -
141H THR* 3.1 37.2 + - + +
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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