Contacts of the strand formed by residues 100 - 107 (chain C) in PDB entry 4LIJ
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 MSE 100 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138A ASP 5.6 0.9 - - - -
139A SER 5.5 1.6 - - - -
142A LEU* 5.9 8.1 - - + -
98C SER* 4.2 7.6 - - - +
99C VAL* 1.3 75.3 - - - +
101C THR* 1.3 70.9 + - - +
102C GLU* 3.6 40.6 - - + +
150C THR* 3.3 4.2 - - - +
151C GLY 2.8 38.6 + - - +
153C PRO* 4.4 18.4 - - + -
156C VAL* 4.1 16.8 - - - -
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Residues in contact with THR 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 4.8 2.0 - - - +
136A ALA* 3.7 7.7 - - + +
138A ASP 4.0 5.2 + - - -
146A SER* 3.6 29.3 + - - +
100C MSE 1.3 83.8 - - - +
102C GLU* 1.3 65.2 + - - +
148C MSE 3.3 35.2 - - + -
149C LEU 3.2 3.4 - - - +
150C THR* 2.9 25.0 + - - +
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Residues in contact with GLU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 5.1 0.2 - - - -
100C MSE 3.6 30.2 - - + +
101C THR* 1.3 76.5 - - - +
103C GLU* 1.3 68.7 + - - +
148C MSE 3.5 3.3 - - - +
149C LEU* 2.8 43.2 + - + +
156C VAL* 4.0 18.4 - - + +
160C LYS* 2.6 37.2 + - - -
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Residues in contact with GLU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR* 4.7 2.6 - - - +
103A GLU* 3.1 47.3 + - + +
148A MSE 3.5 23.0 - - - +
102C GLU* 1.3 84.5 - - - +
104C TYR* 1.3 61.9 + - - +
105C LYS* 3.1 26.7 + - - +
146C SER* 3.5 11.5 + - - -
147C CYS 3.4 14.9 - - - +
148C MSE 4.7 0.2 - - - +
160C LYS* 5.4 0.2 + - - -
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Residues in contact with TYR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLU* 1.3 77.3 - - - +
105C LYS* 1.3 90.8 + - + +
106C VAL* 4.4 7.4 - - + -
146C SER* 3.6 4.0 - - - -
147C CYS* 2.7 38.1 + - + +
149C LEU* 3.8 33.0 - - + -
160C LYS* 3.7 43.2 + - + +
163C LEU* 4.0 26.9 - - + -
164C ASP* 3.3 25.2 + - - -
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Residues in contact with LYS 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C GLU* 3.1 33.7 + - - +
104C TYR* 1.3 101.1 + - - +
106C VAL* 1.3 68.3 + - - +
107C PRO* 5.0 0.2 - - - +
144C GLU* 4.0 30.3 - - + +
145C ARG 3.4 4.7 - - - +
146C SER* 3.4 23.8 + - - +
147C CYS 4.8 0.2 - - - +
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Residues in contact with VAL 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C TYR* 4.4 13.2 - - + -
105C LYS* 1.3 78.7 - - - +
107C PRO* 1.3 75.2 - - + +
111C VAL* 4.0 24.0 - - + -
114C ILE* 3.9 25.1 - - + -
135C ILE* 5.0 3.4 - - + -
144C GLU* 3.3 6.4 - - - +
145C ARG* 2.7 32.0 + - + +
147C CYS* 3.7 27.4 - - - -
163C LEU* 4.5 14.1 - - + -
167C VAL* 5.3 2.7 - - + -
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Residues in contact with PRO 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C LYS 5.0 0.4 - - - +
106C VAL* 1.3 88.4 - - + +
108C ASP* 1.3 67.3 + - - +
109C GLY* 4.4 3.6 - - - +
110C MSE 3.0 33.6 + - + +
111C VAL* 3.5 10.6 + - - +
143C PRO 3.7 3.8 - - - +
144C GLU* 3.4 17.0 - - - +
167C VAL* 4.0 28.9 - - + -
171C ARG* 6.2 0.9 - - - +
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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