Contacts of the strand formed by residues 111 - 115 (chain C) in PDB entry 4ERQ
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 LEU 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C HIS* 4.2 0.4 - - - -
103C VAL* 3.9 15.3 - - + -
104C SER 3.0 15.5 - - - +
105C ALA* 4.1 0.9 - - + -
110C THR* 1.3 74.9 - - - +
112C LYS* 1.3 66.2 + - - +
124C THR* 3.5 1.7 - - - +
125C LEU* 2.7 45.2 + - + +
128C HIS* 4.1 4.9 - - + -
132C VAL* 3.7 20.9 - - + -
135C CYS* 3.6 31.9 - - + -
144C ILE* 4.7 3.4 - - + -
146C SER* 3.7 31.2 - - - +
156C TRP* 3.8 25.8 - - + +
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Residues in contact with LYS 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C GLY* 3.8 21.9 + - - -
86C HIS* 3.6 23.5 - - + +
87C LYS* 6.2 1.6 - - - -
103C VAL* 3.2 4.8 - - - -
104C SER* 3.0 31.8 + - - +
108C ASP* 4.6 2.2 - - - -
110C THR* 4.2 3.4 - - - -
111C LEU* 1.3 80.5 - - - +
113C ILE* 1.3 62.6 + - - +
114C TRP* 3.3 45.3 - - + +
121C CYS* 3.8 12.9 - - - +
123C LYS 3.4 3.8 - - - +
124C THR* 2.8 39.2 + - + +
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Residues in contact with ILE 113 (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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101C LEU* 4.1 28.3 - - + -
102C LEU 3.3 9.2 - - - +
103C VAL* 4.5 0.9 - - + -
112C LYS* 1.3 74.5 - - - +
114C TRP* 1.3 61.7 + - - +
121C CYS* 3.7 3.1 - - - -
122C LEU* 2.8 36.4 + - + -
123C LYS* 3.0 31.8 + - + +
125C LEU* 4.1 28.9 - - + -
137C PHE* 4.7 4.0 - - + -
144C ILE* 3.7 30.1 - - + -
158C VAL* 4.2 18.2 - - + +
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Residues in contact with TRP 114 (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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69C ILE* 3.7 18.7 - - + +
83C ILE* 3.3 36.8 - - + -
84C SER* 3.3 35.9 - - - -
85C GLY* 3.9 4.0 - - - -
86C HIS* 4.0 13.5 - + - -
90C ILE* 5.9 0.2 - - + -
101C LEU* 3.2 13.6 - - - +
102C LEU* 2.8 48.7 + - + +
104C SER* 2.8 20.6 + - - -
112C LYS* 3.3 45.8 + - + +
113C ILE* 1.3 73.7 - - - +
115C ASP* 1.3 63.7 + - - +
116C VAL 3.5 0.8 + - - +
119C GLY 3.6 6.5 - - - -
120C LYS 3.4 4.7 - - - +
121C CYS* 3.6 35.7 - - + -
122C LEU* 4.5 1.1 - - - -
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Residues in contact with ASP 115 (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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100C ASN* 3.8 11.7 - - - +
101C LEU* 4.1 7.5 - - - +
114C TRP* 1.3 70.9 - - - +
116C VAL* 1.3 54.4 + - - +
117C SER* 3.8 8.1 + - - -
118C SER* 2.7 41.8 + - - +
119C GLY* 2.7 35.7 + - - -
120C LYS 2.9 11.1 + - - +
122C LEU* 4.0 24.3 - - + +
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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