Contacts of the strand formed by residues 140 - 152 (chain C) in PDB entry 1DWK
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 GLU 140 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132C LYS* 3.5 34.5 + - + +
133C VAL 3.6 6.3 - - - +
134C ALA* 5.2 3.4 - - - -
135C ASP 4.0 0.2 - - - +
139C GLY* 1.4 80.8 - - - +
141C ARG* 1.3 66.7 + - - +
116H PHE* 3.8 22.6 - - + +
149H LYS* 3.5 11.4 - - - +
150H TYR* 2.9 49.8 + - + +
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Residues in contact with ARG 141 (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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132C LYS* 3.5 5.0 - - - -
133C VAL* 2.7 46.2 + - + +
134C ALA 5.0 1.8 - - - -
135C ASP* 2.9 51.6 + - + +
136C PRO* 5.3 3.1 - - - -
140C GLU* 1.3 80.0 - - - +
142C ALA* 1.3 59.7 + - - +
143C VAL* 5.3 0.9 - - + -
116H PHE* 3.5 7.3 - - - -
125H ASN* 2.9 44.1 + - - +
126H PHE* 3.9 2.0 - - - +
127H LYS* 4.5 3.2 - - - +
147H ASP* 2.7 53.3 + - - +
148H GLY 3.3 7.4 - - - +
149H LYS* 3.6 9.7 - - + +
150H TYR 4.2 0.7 - - - +
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Residues in contact with ALA 142 (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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130C VAL* 4.6 2.9 - - + -
131C LYS 3.3 5.8 - - - +
141C ARG* 1.3 74.3 - - - +
143C VAL* 1.3 61.4 + - - +
144C ILE* 3.9 17.5 - - + +
116H PHE* 3.6 15.1 - - + -
121H ILE* 3.5 35.1 - - + +
146H LEU 3.3 5.5 - - - +
147H ASP* 3.4 2.1 - - - +
148H GLY 2.8 33.1 + - - -
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Residues in contact with VAL 143 (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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129C ASP 3.8 1.6 - - - +
130C VAL* 3.8 0.5 - - - -
131C LYS* 2.9 44.8 + - + +
133C VAL* 3.7 29.8 - - + -
141C ARG* 5.3 1.3 - - + -
142C ALA* 1.3 76.2 - - - +
144C ILE* 1.3 61.0 + - - +
145C THR* 4.0 11.3 + - - +
145H THR* 3.6 29.4 - - + -
146H LEU 3.4 2.5 - - - -
147H ASP* 4.3 17.0 - - - +
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Residues in contact with ILE 144 (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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97C PHE* 3.6 32.8 - - + -
100C MSE 5.9 0.2 - - + -
128C LEU* 4.8 2.9 - - + -
129C ASP 3.3 10.5 - - - +
130C VAL* 4.0 22.2 - - + -
142C ALA* 3.9 20.6 - - + -
143C VAL* 1.3 75.8 - - - +
145C THR* 1.3 61.7 + - - +
146C LEU* 4.2 13.0 - - + -
108H LEU* 4.2 19.3 - - + -
112H VAL* 5.3 1.3 - - + -
121H ILE* 4.4 9.4 - - + -
144H ILE 3.7 1.2 - - - +
145H THR* 3.7 1.6 - - - -
146H LEU* 2.8 59.4 + - + +
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Residues in contact with THR 145 (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 3.9 0.2 - - - +
128C LEU* 3.1 26.2 - - - +
129C ASP* 3.0 29.4 + - - +
131C LYS* 5.6 2.8 - - - +
143C VAL* 4.2 16.1 + - - +
144C ILE* 1.3 73.1 - - - +
146C LEU* 1.3 64.5 + - - +
147C ASP* 4.7 7.9 - - + +
143H VAL* 3.5 32.1 - - + -
144H ILE 3.6 4.0 - - - +
145H THR* 4.5 5.7 + - - +
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Residues in contact with LEU 146 (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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108C LEU* 6.3 0.4 - - + -
126C PHE* 3.9 17.0 - - + -
127C LYS 3.9 3.6 - - - -
128C LEU* 4.0 26.7 - - + -
144C ILE* 4.2 11.4 - - + -
145C THR* 1.3 74.5 - - - +
147C ASP* 1.3 59.1 + - - +
148C GLY 4.1 1.1 - - - -
97H PHE* 4.3 11.4 - - + -
100H MSE 4.1 20.2 - - + -
108H LEU* 6.2 1.3 - - + -
142H ALA 3.5 2.3 - - - +
143H VAL* 3.5 2.1 - - - -
144H ILE* 2.8 60.1 + - + +
146H LEU* 3.9 28.7 - - + -
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Residues in contact with ASP 147 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 3.2 4.8 - - - -
127C LYS* 2.9 57.7 + - + +
145C THR* 4.7 12.3 - - + +
146C LEU* 1.3 73.4 - - - +
148C GLY* 1.3 60.2 + - - +
141H ARG* 2.7 50.2 + - - +
142H ALA 3.4 4.4 - - - +
143H VAL* 4.3 14.2 - - + +
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Residues in contact with GLY 148 (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 ILE* 3.7 20.2 - - - +
122C SER 3.7 9.0 - - - -
125C ASN 3.4 8.3 - - - -
126C PHE* 3.9 2.0 - - - -
146C LEU 4.1 0.6 - - - -
147C ASP* 1.3 76.4 + - - +
149C LYS* 1.3 65.0 + - - -
141H ARG* 3.3 6.8 - - - -
142H ALA 2.8 37.7 + - - +
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Residues in contact with LYS 149 (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 ILE* 3.5 1.1 - - - -
122C SER* 2.8 29.6 + - - -
125C ASN* 3.0 43.6 + - + +
148C GLY* 1.3 72.6 - - - -
150C TYR* 1.3 72.6 + - - +
151C LEU* 3.6 14.4 + - + +
135H ASP* 3.1 22.0 + - - +
138H GLY 3.3 27.5 + - - -
139H GLY* 3.9 4.4 - - - -
140H GLU 3.3 25.6 - - - +
141H ARG* 3.6 6.0 - - - +
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Residues in contact with TYR 150 (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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112C VAL* 5.0 2.0 - - + -
116C PHE* 3.2 65.1 + + + -
117C GLY* 3.3 10.9 - - - -
118C ASP 2.7 28.9 + - - -
119C GLY* 4.2 3.1 - - - -
120C ILE 3.3 18.4 - - - -
121C ILE* 3.9 6.7 - - + +
148C GLY 3.6 2.0 + - - -
149C LYS* 1.3 80.6 - - - +
151C LEU* 1.3 74.4 + - - +
152C PRO* 3.5 29.1 - - + +
140H GLU* 2.9 39.5 + - + +
141H ARG* 4.2 0.4 - - - +
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Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119C GLY* 3.3 1.0 - - - -
120C ILE* 2.9 38.1 + - + -
122C SER* 4.7 2.7 - - - -
125C ASN* 5.8 2.5 - - + +
149C LYS* 3.6 26.9 + - + +
150C TYR* 1.3 85.8 - - - +
152C PRO* 1.3 69.8 - - + +
202C OXL 3.4 32.5 - - - +
122I SER* 4.1 6.1 - - - +
124I ILE* 3.6 14.5 - - + +
125I ASN* 4.7 10.8 - - + +
151I LEU* 3.6 25.1 - - + -
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Residues in contact with PRO 152 (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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118C ASP 3.4 6.7 - - - +
150C TYR* 3.5 31.9 - - + +
151C LEU* 1.3 86.8 - - + +
153C THR* 1.3 60.7 + - - +
154C LYS* 3.8 38.2 + - + +
124I ILE* 3.5 17.3 - - - +
125I ASN* 4.9 2.6 + - - +
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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