Contacts of the strand formed by residues 132 - 140 (chain H) in PDB entry 5LS6
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 132 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G PHE* 6.2 0.2 - - - -
94G GLN* 2.7 29.9 + - - -
86H ASN* 3.7 11.7 - - + +
88H LEU* 3.6 30.3 - - + +
113H PHE* 4.2 7.9 - - + -
124H TYR* 3.5 39.7 - - + -
125H GLU 3.3 9.0 - - - +
126H CYS* 4.2 7.6 - - - -
130H GLY 3.4 1.6 + - - -
131H GLU* 1.3 80.7 - - - +
133H ARG* 1.3 55.4 + - - +
426H ILE* 4.3 12.8 - - + -
434H ILE* 5.2 2.2 - - + -
436H ARG* 3.7 40.2 - - + +
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Residues in contact with ARG 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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70G ILE* 5.5 4.3 - - + -
94G GLN* 3.7 8.3 - - - +
124H TYR* 3.4 4.0 - - - -
125H GLU* 2.6 48.2 + - + +
127H HIS* 3.0 47.1 + - + +
131H GLU* 3.1 35.0 + - - +
132H ILE* 1.3 73.8 - - - +
134H LEU* 1.3 63.9 + - - +
135H LEU* 3.3 14.7 - - + +
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Residues in contact with LEU 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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70G ILE* 4.9 2.9 - - - +
83G CYS* 4.0 10.3 - - + +
85G VAL* 3.3 26.0 - - + -
94G GLN* 2.7 37.2 + - + +
96G ILE* 3.9 37.2 - - + +
122H THR* 3.5 32.3 - - + -
123H LEU 3.6 8.1 - - - +
124H TYR* 3.6 20.4 - - + -
133H ARG* 1.3 73.6 - - - +
135H LEU* 1.3 62.7 + - - +
136H GLN 4.2 5.8 - - - +
137H SER* 5.1 1.1 - - - -
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Residues in contact with LEU 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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68G VAL* 3.7 35.7 - - + +
69G HIS 4.3 2.2 - - - +
70G ILE* 3.4 45.1 - - + +
71G LEU 5.1 1.7 - - - +
96G ILE* 3.5 23.1 - - - +
112H VAL* 3.9 12.8 - - + -
123H LEU* 3.2 16.7 + - + +
124H TYR* 4.2 3.1 - - - -
125H GLU* 3.5 25.4 - - + +
133H ARG* 3.3 22.7 - - + +
134H LEU* 1.3 75.1 - - - +
136H GLN* 1.3 73.7 + - + +
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Residues in contact with GLN 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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69G HIS 4.3 12.6 - - - +
70G ILE* 5.1 2.7 - - - -
71G LEU 5.4 2.0 - - - +
96G ILE* 4.3 7.0 - - - -
122H THR* 3.4 6.3 - - - +
123H LEU* 2.8 41.2 + - + +
134H LEU* 4.0 1.5 - - - +
135H LEU* 1.3 90.5 - - + +
137H SER* 1.3 58.8 + - - +
138H TYR* 3.0 39.1 + - + -
177H PRO* 3.1 26.4 + - - +
180H MET* 3.0 42.4 - - - +
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Residues in contact with SER 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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83G CYS* 3.3 30.2 - - - -
96G ILE* 4.0 10.0 - - - +
97G PRO 3.8 1.7 - - - +
98G LEU* 3.5 10.1 - - - +
99G LYS* 3.1 23.4 + - - +
120H ARG* 3.4 9.2 - - - -
121H VAL 3.5 5.3 + - - -
122H THR* 2.6 33.7 + - - +
134H LEU* 5.1 0.7 - - - -
136H GLN* 1.3 76.7 - - - +
138H TYR* 1.3 61.8 + - - +
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Residues in contact with TYR 138 (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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99G LYS* 3.6 25.8 - - + -
101G LEU* 3.9 31.5 - - + +
120H ARG* 3.0 25.6 - - - +
121H VAL* 2.9 32.3 + - + +
123H LEU* 4.7 11.2 - - + -
136H GLN* 3.0 47.8 + - + -
137H SER* 1.3 74.7 - - - +
139H VAL* 1.3 61.4 + - - +
163H LEU* 6.2 0.7 - - + -
175H ILE* 3.4 24.0 - - + -
177H PRO* 3.3 12.5 - - + +
180H MET* 3.1 31.4 - - + +
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Residues in contact with VAL 139 (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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81G ARG* 4.6 20.4 - - - +
98G LEU* 3.5 36.3 - - + -
99G LYS 2.8 13.8 + - - +
100G THR* 3.4 6.3 - - + +
101G LEU* 2.5 36.5 + - - -
119H ASN* 3.5 15.9 - - - +
120H ARG* 3.7 21.3 - - + +
138H TYR* 1.3 76.7 - - - +
140H ASP* 1.3 72.4 - - - +
141H ALA* 5.0 1.3 - - - -
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Residues in contact with ASP 140 (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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101G LEU* 3.6 10.1 - - - +
103G ALA* 5.1 0.9 + - - -
104G VAL* 4.7 1.7 + - - +
119H ASN* 2.9 33.0 + - + +
139H VAL* 1.3 77.7 - - - +
141H ALA* 1.3 77.3 + - - +
142H ASP* 3.1 17.3 + - - +
145H GLU* 3.2 37.3 - - + +
147H PHE* 3.8 18.8 - - + -
169H ARG* 4.5 3.5 + - - -
173H ARG* 2.6 41.2 + - - +
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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