Contacts of the strand formed by residues 127 - 133 (chain A) in PDB entry 3EJW
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 ALA 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A VAL* 3.7 29.8 - - + -
124A LYS* 4.3 1.1 - - - +
125A GLU 3.9 0.8 + - - -
126A LYS* 1.3 77.2 - - - +
128A LYS* 1.3 60.9 + - - +
129A VAL* 4.8 2.9 - - + -
158A GLY 3.3 7.0 + - - +
159A TRP* 3.3 16.8 - - + +
160A GLU* 2.7 34.0 + - - +
189A ASP* 3.1 17.7 - - + +
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Residues in contact with LYS 128 (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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126A LYS* 5.9 7.4 - - - +
127A ALA* 1.3 79.0 - - - +
129A VAL* 1.3 61.5 + - - +
160A GLU* 3.3 23.1 - - + +
162A VAL* 3.7 23.6 - - + -
185A TYR* 5.6 5.4 - - + -
187A ASP* 2.7 48.2 + - - +
188A LEU* 3.6 9.4 - - + +
189A ASP* 2.9 36.5 + - - +
190A ALA 3.2 5.9 + - - -
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Residues in contact with VAL 129 (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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122A VAL* 5.5 0.4 - - + -
127A ALA* 4.7 3.8 - - + -
128A LYS* 1.3 82.6 - - - +
130A ALA* 1.3 70.5 + - - +
131A PHE* 4.6 0.9 - - + -
159A TRP* 3.7 38.8 - - + -
160A GLU 2.8 8.7 + - - -
161A ILE* 3.3 25.3 - - + +
162A VAL 2.9 25.5 + - - +
188A LEU* 4.1 3.6 - - - +
190A ALA* 3.4 20.9 - - + +
192A ILE* 3.7 31.9 - - + -
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Residues in contact with ALA 130 (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 VAL* 1.3 78.5 - - - +
131A PHE* 1.3 64.9 + - - +
163A THR* 3.4 28.7 - - + -
181A ILE* 3.9 23.1 - - + -
188A LEU* 3.9 8.7 - - + +
190A ALA 2.8 13.9 + - - +
191A ILE* 3.3 6.7 - - + +
192A ILE* 2.8 27.0 + - - +
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Residues in contact with PHE 131 (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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114A LEU* 5.3 1.3 - - + -
129A VAL* 4.6 0.7 - - + -
130A ALA* 1.3 78.4 - - - +
132A PHE* 1.3 62.1 + - - +
133A TYR* 4.3 5.8 - + + -
145A ALA* 4.1 25.6 - - + -
148A ALA* 3.8 28.3 - - + -
149A LYS* 3.9 21.1 - - + -
152A ILE* 3.8 26.5 - - + -
161A ILE* 3.9 24.0 - - + -
163A THR 2.9 8.0 + - - +
164A THR* 3.3 25.0 - - + +
165A GLN 3.0 23.5 + - - -
181A ILE* 4.6 1.9 - - - +
192A ILE* 3.4 37.7 - - + -
194A PRO* 4.9 2.2 - - + -
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Residues in contact with PHE 132 (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 PHE* 1.3 76.8 - - - +
133A TYR* 1.3 65.5 + - - +
165A GLN 3.3 11.9 - - - -
167A GLY* 3.8 17.0 - - - -
174A SER* 3.3 34.3 - - - -
177A THR* 3.4 28.0 - - + -
178A ALA* 3.9 20.0 - - + -
181A ILE* 4.1 13.9 - - + -
191A ILE* 4.0 18.8 - - + -
192A ILE 3.0 6.1 + - - -
193A ALA* 3.0 28.6 - - + +
198A ALA* 3.2 36.8 - - + +
201A ALA* 4.3 0.2 - - + -
202A ALA* 4.1 13.2 - - + -
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Residues in contact with TYR 133 (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 PHE* 4.3 4.9 - - + -
132A PHE* 1.3 85.6 - - - +
134A SER* 1.3 67.1 + - - +
135A SER 3.5 16.2 - - - -
141A GLN* 3.2 26.9 - - + +
142A ASN* 2.8 37.8 + - - -
145A ALA* 3.6 29.2 - - + +
149A LYS* 5.0 3.2 + - - -
164A THR* 3.9 21.5 - - + +
165A GLN 3.2 5.1 + - - -
166A TYR* 3.1 23.5 + + - -
167A GLY 2.8 23.2 + - - -
194A PRO* 3.9 25.4 - - + -
195A ASP* 3.9 13.2 - - + -
198A ALA* 4.0 5.2 - - - -
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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