Contacts of the strand formed by residues 137 - 144 (chain A) in PDB entry 5CEO
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 GLY 137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A GLY 3.8 0.3 - - - +
133A SER* 3.2 26.2 - - - -
134A GLY 3.5 6.4 + - - -
136A GLN* 1.3 95.0 + - - +
138A ALA* 1.3 62.7 + - - -
139A VAL* 3.5 6.0 + - - +
152A LYS* 5.2 1.1 - - - -
153A LYS 4.8 8.3 - - - -
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Residues in contact with ALA 138 (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 TRP* 4.5 4.9 - - - +
132A GLY 3.9 0.4 - - - -
133A SER* 3.7 15.2 + - - +
137A GLY* 1.3 68.7 - - - -
139A VAL* 1.3 59.0 + - - +
140A PHE* 3.9 20.0 - - + -
151A VAL 3.9 0.7 - - - +
152A LYS* 3.8 1.2 - - - +
153A LYS* 2.9 45.4 + - + +
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Residues in contact with VAL 139 (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 TRP* 3.5 6.6 - - - -
131A VAL* 2.9 37.2 + - + +
132A GLY 2.9 12.1 + - - +
136A GLN 4.3 2.5 - - - +
137A GLY 3.8 6.7 - - - +
138A ALA* 1.3 77.9 - - - +
140A PHE* 1.3 71.1 + - - +
150A ALA* 4.5 3.6 - - + -
151A VAL 3.7 9.2 - - - +
152A LYS* 4.1 11.4 - - + -
501A 50D 3.4 72.9 - - + +
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Residues in contact with PHE 140 (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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128A LEU* 3.8 30.5 - - + -
129A GLN* 3.3 12.8 - - - +
130A TRP* 3.4 42.2 - + + -
131A VAL* 4.2 6.0 - - - +
138A ALA* 3.9 28.0 - - + -
139A VAL* 1.3 78.3 - - - +
141A LEU* 1.3 58.9 + - - +
150A ALA* 3.4 6.4 - - - -
151A VAL* 2.8 45.0 + - + +
153A LYS* 4.5 11.0 - - + -
192A PHE* 5.1 0.2 - - - -
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Residues in contact with LEU 141 (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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127A ASP 3.2 4.7 - - - +
128A LEU* 3.4 1.8 - - - -
129A GLN* 2.7 54.1 + - + +
131A VAL* 3.8 20.3 - - + +
140A PHE* 1.3 74.0 - - - +
142A GLY* 1.3 68.3 + - - +
148A GLU* 4.1 26.9 - - + +
149A VAL 3.4 15.7 - - - +
192A PHE* 3.7 41.5 - - + -
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Residues in contact with GLY 142 (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 ILE* 5.3 0.7 - - - -
126A LEU 3.3 11.7 - - - -
127A ASP* 4.0 3.1 - - - -
128A LEU* 4.3 11.9 - - - -
140A PHE 4.0 1.0 + - - -
141A LEU* 1.3 79.0 - - - +
143A ARG* 1.3 57.7 + - - +
148A GLU* 3.5 6.6 - - - +
149A VAL* 2.8 41.1 + - - +
151A VAL* 4.5 1.9 - - - +
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Residues in contact with ARG 143 (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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124A GLU 3.4 4.2 - - - +
125A ILE* 3.9 1.4 - - - -
126A LEU* 2.8 65.6 + - + +
127A ASP* 2.8 38.6 + - + +
142A GLY* 1.3 74.1 - - - +
144A PHE* 1.3 64.1 + - - +
146A GLY* 4.2 18.4 - - - +
147A GLU 3.3 20.9 - - - +
148A GLU* 5.3 2.2 - - + -
149A VAL* 4.3 1.1 - - - +
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Residues in contact with PHE 144 (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 LEU 5.5 2.5 - - - -
120A VAL* 3.4 36.3 - - + -
124A GLU* 3.6 33.9 - - + +
125A ILE* 4.8 2.9 - - - -
143A ARG* 1.3 75.8 - - - +
145A HIS* 1.3 109.1 - + + +
146A GLY 3.3 0.9 - - - -
147A GLU* 2.9 24.2 + - - +
149A VAL* 3.8 27.9 - - + +
177A LYS* 4.4 17.9 - - + -
189A LEU* 3.7 20.9 - - + -
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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