Contacts of the strand formed by residues 218 - 225 (chain A) in PDB entry 3W5D
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 LYS 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LYS* 6.1 0.2 - - - +
152A GLU* 3.4 36.9 + - + -
153A VAL 3.5 13.2 - - - +
154A ALA* 4.1 12.8 - - + +
168A ILE* 3.8 3.3 - - - +
169A LYS* 3.1 44.9 + - + +
170A SER* 2.7 19.4 + - - +
173A LEU* 3.8 2.6 - - - +
217A GLY* 1.3 75.1 - - - +
219A ALA* 1.3 67.6 + - - +
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Residues in contact with ALA 219 (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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151A VAL 4.1 0.2 - - - +
152A GLU* 3.5 7.7 - - - +
153A VAL* 2.9 45.4 + - + +
165A ILE* 4.3 9.9 - - + -
167A SER 3.5 9.6 - - - +
168A ILE* 4.3 5.4 - - - -
169A LYS* 4.3 4.0 - - - +
173A LEU* 3.6 30.2 - - + +
208A LEU* 5.2 2.2 - - + -
218A LYS* 1.3 78.0 - - - +
220A LEU* 1.3 61.3 + - - +
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Residues in contact with LEU 220 (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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20A GLU* 3.9 37.0 - - + +
130A TYR* 3.8 26.5 - - + -
150A ILE* 3.7 22.2 - - + -
151A VAL 3.4 14.8 - - - +
152A GLU* 4.4 6.7 - - + +
165A ILE* 3.8 4.0 - - - +
166A LEU* 2.8 21.6 + - + -
167A SER* 2.6 29.6 + - - +
169A LYS* 4.2 24.2 - - + +
208A LEU* 6.5 0.7 - - - -
219A ALA* 1.3 76.2 - - - +
221A GLY* 1.3 59.8 - - - +
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Residues in contact with GLY 221 (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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150A ILE* 3.4 5.9 - - - +
151A VAL* 2.7 41.3 + - - +
163A ILE* 3.8 13.9 - - - +
164A ARG 3.2 12.3 - - - -
165A ILE* 4.1 1.1 - - - -
166A LEU* 3.5 12.6 - - - -
208A LEU* 6.3 0.8 - - - +
220A LEU* 1.3 76.5 - - - +
222A ILE* 1.3 58.5 + - - -
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Residues in contact with ILE 222 (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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12A CYS* 3.5 37.7 - - + +
13A LEU* 4.1 4.5 - - + -
16A PHE* 3.9 13.5 - - + -
18A VAL* 3.7 23.6 - - + -
148A GLY* 3.6 20.6 - - - +
149A ASP 3.5 2.2 - - - +
150A ILE* 4.2 3.4 - - + -
163A ILE* 3.9 2.7 - - - -
164A ARG* 2.7 54.5 + - + +
166A LEU* 3.7 28.5 - - + +
221A GLY* 1.3 75.0 - - - +
223A VAL* 1.3 65.7 + - - +
224A ALA* 3.3 0.6 + - - -
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Residues in contact with VAL 223 (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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16A PHE* 3.8 7.3 - - - -
145A ILE* 3.8 21.8 - - + -
146A VAL 3.5 21.3 - - - +
147A PRO* 3.5 4.7 - - + +
148A GLY* 2.9 25.6 + - - -
149A ASP* 3.1 16.6 + - + +
151A VAL* 3.8 11.7 - - + -
160A PRO* 6.4 0.2 - - + -
161A ALA* 4.0 3.8 - - + -
162A ASP 3.6 6.1 - - - +
163A ILE* 3.8 18.4 - - + -
222A ILE* 1.3 68.7 - - - +
224A ALA* 1.3 62.8 + - - +
225A THR 3.5 21.3 - - - +
226A THR* 3.6 14.4 - - + -
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Residues in contact with ALA 224 (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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0A ACE 3.6 3.1 - - - +
1A MET* 2.7 43.3 + - - +
4A ALA* 3.5 31.9 - - + -
16A PHE* 4.1 3.1 - - - -
147A PRO* 4.3 1.7 - - - +
162A ASP 2.9 11.4 + - - +
164A ARG* 4.5 1.1 - - + +
207A MET* 4.1 14.6 - - + -
222A ILE* 3.3 7.1 + - - +
223A VAL* 1.3 73.6 - - - +
225A THR* 1.4 61.4 + - + +
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Residues in contact with THR 225 (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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0A ACE 4.2 3.4 - - + -
1A MET 3.9 14.6 - - - +
2A GLU* 3.9 27.1 - - + +
147A PRO* 4.5 6.1 - - - -
162A ASP* 3.3 45.2 + - - +
223A VAL* 3.5 2.6 - - - +
224A ALA* 1.4 86.9 - - + +
226A THR* 1.3 70.8 + - - +
229A SER* 3.6 31.6 + - - +
230A THR* 3.7 3.1 - - - -
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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