Contacts of the strand formed by residues 120 - 126 (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 ARG 120 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83G CYS* 3.2 15.3 - - - +
98G LEU* 4.4 13.7 - - - +
90H GLU* 4.4 0.4 - - - +
91H ASP* 2.7 39.6 + - - -
92H HIS* 3.9 32.9 - - + +
96H LEU* 5.3 0.7 - - - +
115H THR 3.5 3.5 - - - +
117H GLY 2.9 40.3 + - - +
118H SER* 3.3 3.0 + - - -
119H ASN* 1.3 85.0 + - - +
121H VAL* 1.3 59.0 + - - +
122H THR* 3.5 12.6 - - - +
137H SER* 3.4 18.6 - - - +
138H TYR 3.0 17.5 - - - +
139H VAL* 3.7 16.4 - - + +
147H PHE* 3.6 8.0 - - - -
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Residues in contact with VAL 121 (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* 4.9 5.6 - - + -
114H ALA* 4.4 5.4 - - + -
115H THR 3.6 5.4 - - - +
116H VAL* 4.0 15.7 - - + -
120H ARG* 1.3 71.9 - - - +
122H THR* 1.3 63.4 + - - +
123H LEU* 4.0 7.6 - - + -
137H SER* 3.5 0.2 - - - -
138H TYR* 2.9 57.9 + - + +
147H PHE* 4.5 4.8 - - + -
163H LEU* 3.3 32.1 - - + -
165H VAL* 3.9 21.8 - - + -
175H ILE* 4.5 11.9 - - + -
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Residues in contact with THR 122 (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* 4.3 3.6 - - - -
90H GLU* 2.7 30.8 + - - +
114H ALA* 3.6 1.0 - - - -
115H THR* 2.8 35.0 + - - -
120H ARG* 3.5 7.1 - - - +
121H VAL* 1.3 73.3 - - - +
123H LEU* 1.3 64.3 + - - +
124H TYR* 3.6 16.1 - - + +
134H LEU* 3.5 24.0 - - + -
136H GLN 3.4 13.2 - - - +
137H SER* 2.6 25.4 + - - +
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Residues in contact with LEU 123 (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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112H VAL* 4.9 9.0 - - + -
113H PHE 3.6 3.8 - - - +
114H ALA* 4.2 2.9 - - + -
121H VAL* 4.0 6.5 - - + -
122H THR* 1.3 76.6 - - - +
124H TYR* 1.3 70.2 + - - +
134H LEU* 3.6 8.3 - - - +
135H LEU* 3.2 29.7 + - + -
136H GLN* 2.8 42.4 + - + +
138H TYR* 4.7 12.3 - - + -
152H TRP* 3.7 28.7 - - + -
163H LEU* 3.8 27.6 - - + -
177H PRO* 4.1 13.9 - - + -
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Residues in contact with TYR 124 (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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85G VAL* 3.9 22.1 - - + +
88H LEU* 4.1 6.7 - - + -
90H GLU* 3.0 35.9 + - - +
112H VAL* 3.0 8.3 - - - +
113H PHE* 2.7 69.7 + + + -
115H THR* 3.6 15.9 - - - -
122H THR* 3.6 18.9 - - + +
123H LEU* 1.3 78.1 - - - +
125H GLU* 1.3 59.0 + - - +
132H ILE* 3.5 25.6 - - + -
133H ARG 3.4 4.9 - - - -
134H LEU* 3.6 27.8 - - + -
135H LEU* 4.2 1.8 - - - -
434H ILE* 3.4 19.0 - - + +
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Residues in contact with GLU 125 (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 19.9 - - + +
70G ILE* 3.8 9.7 - - - +
110H PRO* 3.2 34.4 - - + +
111H LEU 4.1 2.2 - - - -
112H VAL* 4.2 2.9 - - + -
124H TYR* 1.3 73.2 - - - +
126H CYS* 1.3 62.8 + - - +
127H HIS* 2.8 33.9 + - + -
132H ILE* 3.3 4.7 - - - -
133H ARG* 2.6 46.8 + - + +
135H LEU* 3.5 29.9 - - + +
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Residues in contact with CYS 126 (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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101H PHE* 3.9 9.0 - - - -
110H PRO* 4.7 3.8 - - - +
111H LEU* 3.1 32.7 + - + +
113H PHE* 3.9 25.1 - - - -
125H GLU* 1.3 74.9 - - - +
127H HIS* 1.3 64.2 + - - +
131H GLU 4.0 3.4 - - - -
132H ILE* 4.2 11.7 - - - +
424H ILE* 3.6 33.4 - - + -
426H ILE* 4.5 1.1 - - - -
436H ARG* 4.3 12.1 - - - +
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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