Contacts of the strand formed by residues 121 - 129 (chain C) in PDB entry 2Q7N
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 ASN 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120C SER* 1.3 68.8 - - - +
122C ALA* 1.3 60.2 + - - +
123C THR* 4.2 9.7 + - + +
143C ASN 4.1 5.6 - - - +
144C THR* 3.6 16.1 + - - +
175C HIS* 5.1 0.2 - - - -
177C ASP* 3.0 37.9 + - + +
178C SER* 5.4 0.4 - - - +
1M NAG 1.5 71.9 + - - +
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Residues in contact with ALA 122 (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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111C ASP* 6.0 0.4 - - - +
116C LEU* 6.0 1.1 - - + -
120C SER* 2.9 11.8 + - - +
121C ASN* 1.3 72.1 - - - +
123C THR* 1.3 61.4 + - - +
124C TRP* 3.7 10.5 + - + +
143C ASN* 2.4 33.3 + - - +
145C MET* 4.3 12.1 - - + -
174C TRP* 3.9 31.0 - - + -
175C HIS 3.7 6.5 - - - +
176C ILE* 4.0 10.8 - - + +
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Residues in contact with THR 123 (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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121C ASN* 4.2 8.5 + - + +
122C ALA* 1.3 81.1 - - - +
124C TRP* 1.3 63.5 + - - +
140C VAL* 6.1 3.1 - - - -
141C LEU 3.8 8.3 - - - -
142C LEU* 3.4 42.4 - - + +
143C ASN 4.0 1.8 - - - +
174C TRP* 3.1 3.1 - - - -
175C HIS* 2.9 72.9 + - + -
187C TRP* 4.3 2.6 - - - -
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Residues in contact with TRP 124 (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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91C PRO* 4.4 16.4 - - + -
109C TRP* 3.9 50.0 - + + -
110C ASN 3.8 23.8 - - - -
111C ASP* 4.0 20.6 - - - -
112C ARG 4.7 0.4 - - - -
122C ALA* 3.7 9.9 + - + +
123C THR* 1.3 78.1 - - - +
125C GLU* 1.3 63.7 + - - +
126C ILE* 4.3 2.5 - - + -
140C VAL* 3.5 6.1 - - - +
141C LEU* 2.9 39.1 + - + +
143C ASN* 3.5 38.7 + - + +
172C ILE* 4.8 10.3 - - + -
173C ARG 3.3 9.4 - - - +
174C TRP* 3.5 46.2 - + + -
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Residues in contact with GLU 125 (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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124C TRP* 1.3 77.5 - - - +
126C ILE* 1.3 69.6 + - - +
138C ALA* 4.6 12.2 - - + +
139C LEU 3.5 8.5 - - - +
140C VAL* 3.8 22.0 - - + +
172C ILE* 3.3 5.2 - - - -
173C ARG* 2.6 65.8 + - + +
187C TRP* 3.4 25.4 - - + -
190C TRP* 3.6 13.7 - - + -
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Residues in contact with ILE 126 (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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107C LEU* 4.2 15.9 - - + -
109C TRP* 4.4 9.2 - - + +
124C TRP* 5.2 3.1 - - + -
125C GLU* 1.3 79.0 - - - +
127C LYS* 1.3 76.1 + - - +
137C VAL 3.4 2.5 - - - +
138C ALA* 3.2 7.6 - - - +
139C LEU 2.7 43.5 + - - +
141C LEU* 5.2 12.6 - - + -
155C TRP* 3.6 63.5 - - + +
170C VAL* 4.9 2.9 - - + -
171C SER 3.5 10.3 - - - +
172C ILE* 3.3 21.1 - - + -
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Residues in contact with LYS 127 (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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126C ILE* 1.3 76.9 - - - +
128C VAL* 1.3 70.7 + - - +
129C LEU* 4.2 23.8 - - - +
135C GLU* 4.2 19.7 - - + +
137C VAL 3.7 2.7 - - - -
138C ALA* 4.7 5.6 - - + +
170C VAL* 3.2 7.1 - - - +
171C SER* 2.8 57.6 + - - +
190C TRP* 3.7 45.0 - - + +
193C LEU* 4.5 13.1 - - - +
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Residues in contact with VAL 128 (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 LEU* 4.5 2.2 - - + -
127C LYS* 1.3 73.2 - - - +
129C LEU* 1.3 71.7 + - - +
135C GLU* 3.3 13.2 - - - +
136C PRO* 3.2 21.0 - - + +
137C VAL* 2.9 50.5 + - + +
155C TRP* 4.6 11.0 - - + -
157C TRP* 3.7 31.0 - - + -
168C HIS* 5.7 1.6 - - + -
169C SER 3.3 4.5 - - - +
170C VAL* 3.5 24.5 - - + -
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Residues in contact with LEU 129 (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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127C LYS* 4.2 30.5 - - + +
128C VAL* 1.3 83.8 - - - +
130C GLN* 1.3 70.6 + - - +
132C PRO 4.7 6.5 - - - +
133C ARG 5.8 1.8 - - - +
134C THR 4.3 14.1 - - - +
135C GLU* 5.3 2.7 - - + -
136C PRO* 3.5 9.2 - - - -
168C HIS* 3.0 24.4 - - - -
169C SER* 2.8 51.6 + - - +
170C VAL* 4.1 3.4 - - - +
171C SER* 5.4 0.4 - - - -
193C LEU* 5.5 6.5 - - + -
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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