Contacts of the strand formed by residues 155 - 166 (chain A) in PDB entry 1EJ0
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 LEU 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A VAL* 3.4 19.1 - - - +
119A GLN 3.5 17.0 - - - +
120A VAL* 3.8 4.3 - - - +
121A VAL* 3.9 9.0 - - + +
151A CYS* 2.9 47.2 + - - +
154A VAL* 1.3 75.6 - - - +
156A ALA* 1.3 68.9 + - - +
157A PRO* 3.8 1.7 - - - +
159A GLY* 3.8 7.0 - - - -
160A SER 3.4 25.1 - - - +
182A PHE* 3.6 27.1 - - + -
207A ARG* 3.0 32.1 + - + +
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Residues in contact with ALA 156 (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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117A LYS* 4.1 31.9 - - + +
118A VAL 2.9 22.1 + - - +
119A GLN* 5.1 5.6 - - + +
154A VAL 3.4 3.0 + - - +
155A LEU* 1.3 75.2 - - - +
157A PRO* 1.4 83.1 - - + +
159A GLY* 2.9 17.7 + - - +
207A ARG* 3.6 5.6 - - - +
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Residues in contact with PRO 157 (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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117A LYS* 4.1 17.7 + - - +
155A LEU 3.8 2.4 - - - +
156A ALA* 1.4 94.9 - - + +
158A GLY* 1.3 60.2 + - - +
159A GLY 3.3 0.3 + - - -
207A ARG* 3.7 15.9 - - - +
208A LYS 5.0 0.7 - - - +
209A PRO* 5.1 18.4 - - + +
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Residues in contact with GLY 158 (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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157A PRO* 1.3 72.3 - - - +
159A GLY* 1.3 64.8 + - - +
160A SER* 4.9 1.0 + - - -
206A GLY* 3.8 13.7 + - - -
207A ARG 2.8 23.9 + - - -
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Residues in contact with GLY 159 (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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119A GLN* 3.3 17.5 - - - -
155A LEU* 3.8 9.4 - - - -
156A ALA* 2.9 19.4 + - - -
157A PRO 3.2 1.0 + - - -
158A GLY* 1.3 77.6 - - - +
160A SER* 1.3 63.4 + - - -
182A PHE* 3.6 3.8 - - - -
206A GLY 3.1 8.8 + - - -
207A ARG 3.0 21.0 + - - +
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Residues in contact with SER 160 (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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48A LEU* 3.9 22.9 + - - +
119A GLN 2.9 11.7 + - - -
120A VAL* 3.2 18.8 - - - +
121A VAL 3.0 24.5 + - - +
155A LEU* 3.4 8.5 - - - +
158A GLY 4.9 1.0 + - - -
159A GLY* 1.3 76.4 - - - -
161A PHE* 1.3 61.6 + - - +
182A PHE* 4.3 0.2 - - - -
204A ALA 3.1 10.5 - - - -
205A THR* 3.5 17.8 - - - +
206A GLY 4.7 0.3 + - - -
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Residues in contact with PHE 161 (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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48A LEU* 5.6 0.2 - - - -
121A VAL* 3.2 31.2 - - + -
123A SER* 4.8 2.5 - - - -
147A ALA* 4.0 14.8 - - + -
148A LEU* 3.8 36.1 - - + -
151A CYS* 3.8 14.6 - - + -
160A SER* 1.3 78.2 - - - +
162A VAL* 1.3 63.0 + - - +
163A VAL* 3.7 27.6 - - + -
174A TYR* 3.5 26.5 - - - -
178A ILE* 3.9 14.6 - - + -
182A PHE* 3.6 25.3 - + + -
202A ILE* 3.5 2.5 - - + +
203A VAL* 4.8 0.5 - - - +
204A ALA* 2.8 38.8 + - + +
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Residues in contact with VAL 162 (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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39A LEU* 4.9 3.4 - - + -
42A ILE* 4.2 20.9 - - + -
48A LEU* 4.1 23.1 - - + -
49A PHE* 4.8 4.5 - - + -
65A TRP* 4.5 7.6 - - + -
120A VAL* 4.4 5.6 - - + -
121A VAL 3.0 4.6 + - - +
122A MET* 3.3 27.9 - - + -
123A SER 2.8 26.2 + - - +
161A PHE* 1.3 77.7 - - - +
163A VAL* 1.3 63.0 + - - +
201A TYR* 4.4 11.0 - - + -
202A ILE 3.2 8.1 - - - +
203A VAL* 4.1 16.4 - - + -
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Residues in contact with VAL 163 (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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123A SER* 3.4 18.2 - - - +
144A VAL* 3.7 20.4 - - + -
147A ALA* 4.8 0.2 - - + -
161A PHE* 3.7 31.2 - - + -
162A VAL* 1.3 77.7 - - - +
164A LYS* 1.3 75.9 + - - +
165A VAL* 3.5 13.3 + - + +
174A TYR* 3.8 15.9 - - + +
178A ILE* 4.2 0.7 - - + -
201A TYR* 3.3 6.4 - - - -
202A ILE* 3.0 44.8 + - + +
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Residues in contact with LYS 164 (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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38A LYS* 3.8 7.3 - - - +
123A SER* 3.0 12.4 + - - +
124A ASP* 2.9 48.6 + - - +
125A MET 3.9 14.3 - - - +
126A ALA* 3.9 11.7 - - + -
144A VAL* 3.2 23.7 - - - +
163A VAL* 1.3 72.1 - - - +
165A VAL* 1.3 61.6 + - - +
166A PHE* 4.0 25.2 - - + -
199A GLU* 2.8 36.2 + - + +
200A VAL 3.5 7.9 - - - +
201A TYR* 3.0 25.7 + - + +
301A SAM 3.9 11.3 - - - +
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Residues in contact with VAL 165 (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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141A MET* 4.1 22.9 - - - -
144A VAL* 4.3 5.2 - - + -
163A VAL* 3.6 18.4 - - + +
164A LYS* 1.3 81.9 - - - +
166A PHE* 1.3 79.8 + - - +
171A PHE* 3.9 18.4 - - + -
174A TYR* 3.8 31.2 - - + -
199A GLU* 3.4 3.2 - - - -
200A VAL* 2.8 37.4 + - + +
202A ILE* 3.9 12.6 - - + -
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Residues in contact with PHE 166 (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 5.2 1.1 - - - -
126A ALA* 4.2 13.5 - - + -
129A MET* 3.6 32.5 - - + -
137A ILE* 3.5 25.8 - - + +
140A ALA* 3.8 23.8 - - + -
141A MET* 5.2 2.7 - - - +
164A LYS* 4.0 30.1 - - + -
165A VAL* 1.3 91.8 - - - +
167A GLN* 1.3 65.7 + - - +
168A GLY* 3.6 2.6 + - - +
169A GLU 5.0 1.7 - - - +
171A PHE* 3.8 11.9 + - - +
197A SER* 4.7 4.0 - - - -
198A ARG* 3.6 13.2 - - + -
199A GLU* 3.8 29.6 - - + -
200A VAL* 5.4 0.4 - - - -
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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