Contacts of the strand formed by residues 175 - 185 (chain A) in PDB entry 1DLS
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 ILE 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TRP* 4.4 3.4 - - + -
25A PRO* 3.6 38.8 - - + -
27A LEU* 4.5 20.0 - - + -
138A ILE* 3.4 34.3 - - + -
140A GLN* 3.9 24.7 - - + +
142A PHE* 4.0 10.3 - - + -
171A GLU* 3.1 3.2 - - - -
172A GLU 2.7 38.1 + - - +
173A LYS* 4.0 9.9 - - + +
174A GLY* 1.3 77.8 - - - +
176A LYS* 1.3 65.8 + - - +
177A TYR* 3.8 5.0 - - - -
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Residues in contact with LYS 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A MET* 2.7 52.3 + - + +
140A GLN* 5.1 1.8 - - - +
169A VAL* 3.9 19.4 - - + +
170A GLN 3.1 12.8 - - - +
171A GLU* 3.6 32.8 + - + +
174A GLY 4.1 1.3 + - - +
175A ILE* 1.3 76.6 - - - +
177A TYR* 1.3 58.2 + - - +
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Residues in contact with TYR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A LEU* 4.1 19.7 - - + -
29A ASN* 3.3 19.2 + - - +
30A GLU* 3.6 14.1 + - + -
136A THR* 3.7 17.5 - - + -
137A ARG 3.0 14.6 - - - +
138A ILE* 3.6 17.0 - - + -
139A MET* 4.1 4.9 - - - -
169A VAL* 3.7 1.2 - - - -
170A GLN* 2.7 59.4 + - + +
172A GLU* 3.3 41.0 + - + +
175A ILE* 3.8 12.3 - - + -
176A LYS* 1.3 75.8 - - - +
178A LYS* 1.3 61.9 - - - +
179A PHE* 3.6 26.2 - + - -
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A VAL 3.9 0.5 - - - +
136A THR* 3.6 3.5 - - - +
137A ARG* 2.8 52.7 + - + +
139A MET* 4.1 20.8 - - + +
167A SER 5.3 4.3 - - - +
168A ASP 4.5 8.1 - - - +
169A VAL* 4.5 20.4 - - + +
170A GLN* 5.0 0.9 - - - -
177A TYR* 1.3 78.2 - - - +
179A PHE* 1.3 63.0 + - - +
180A GLU* 2.9 35.8 + - + -
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Residues in contact with PHE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ASN* 4.5 6.3 - - + -
30A GLU* 4.0 3.6 - - - -
33A TYR* 3.3 59.7 - + + +
135A VAL 3.7 2.7 - - - -
136A THR* 3.3 32.3 - - + -
165A VAL* 3.7 22.6 - - + +
166A LEU* 3.8 40.7 + - + +
167A SER* 5.3 5.0 + - - +
168A ASP 5.1 1.0 + - - -
170A GLN* 4.2 20.9 - - + -
177A TYR* 3.6 17.9 - + - -
178A LYS* 1.3 74.8 - - - +
180A GLU* 1.3 61.1 + - - +
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Residues in contact with GLU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 5.2 1.0 + - - -
133A LEU 4.3 0.7 - - - -
134A PHE* 3.5 2.4 - - - -
135A VAL 2.7 39.2 + - - +
137A ARG* 2.9 22.2 + - + +
158A LEU* 3.7 26.4 - - + +
178A LYS* 2.9 38.8 + - + -
179A PHE* 1.3 77.6 - - - +
181A VAL* 1.3 67.6 + - - +
182A TYR* 2.7 31.7 + - + -
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TYR* 5.1 0.2 - - - +
132A LYS* 4.4 4.5 - - + -
133A LEU 3.4 5.6 - - - +
134A PHE* 4.0 39.5 - - + -
158A LEU* 3.7 4.9 - - - +
159A LEU* 2.9 51.2 + - + +
161A GLU 5.9 0.2 - - - -
162A TYR* 3.7 33.7 - - + -
165A VAL* 4.2 15.5 - - + -
180A GLU* 1.3 79.5 - - - +
182A TYR* 1.3 66.5 + - - +
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Residues in contact with TYR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU 4.1 0.2 - - - +
132A LYS* 3.2 8.0 - - - +
133A LEU* 2.8 44.8 + - + +
135A VAL* 3.7 30.7 - - + -
137A ARG* 2.9 20.9 + - - -
151A ILE* 4.3 7.9 - - + -
153A LEU* 3.9 21.8 - - + +
156A TYR* 4.1 24.9 - - + -
157A LYS 3.3 6.7 - - - +
158A LEU* 3.6 39.2 - - + +
159A LEU* 4.9 0.2 - - - -
180A GLU* 2.7 37.9 + - + -
181A VAL* 1.3 77.1 - - - +
183A GLU* 1.3 63.3 - - - +
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Residues in contact with GLU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A HIS* 2.8 33.7 + - + +
131A LEU 3.6 2.0 - - - -
132A LYS* 3.9 20.3 + - + +
155A LYS 3.8 1.4 - - - +
156A TYR* 3.7 3.6 - - - -
157A LYS* 2.9 36.7 + - + +
159A LEU* 3.9 31.8 - - + +
162A TYR* 5.7 0.5 - - - -
182A TYR* 1.3 78.4 - - - +
184A LYS* 1.3 65.6 + - - +
185A ASN* 5.9 0.6 - - + +
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Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A MET 3.9 6.5 - - - +
126A ASN 5.2 0.6 + - - -
127A HIS 3.2 26.2 + - - -
129A GLY 2.7 25.1 + - - +
130A HIS* 3.5 9.4 - - - -
131A LEU* 3.0 37.0 + - - +
155A LYS* 3.8 17.7 - - + +
156A TYR* 3.3 47.3 - - + +
183A GLU* 1.3 75.4 - - - +
185A ASN* 1.3 66.6 + - - +
186A ASP* 2.4 43.4 + - - +
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Residues in contact with ASN 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A GLY* 4.0 3.4 - - - -
130A HIS* 3.8 36.9 - - + +
155A LYS 4.8 1.6 + - - -
183A GLU* 5.9 0.9 - - + +
184A LYS* 1.3 76.9 - - - +
186A ASP* 1.5 69.9 + - - +
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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