Contacts of the strand formed by residues 240 - 247 (chain A) in PDB entry 3PEJ
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 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A ASP 3.3 10.1 - - - -
150A GLY 3.3 25.0 + - - -
152A GLY* 4.0 2.7 - - - -
208A THR* 3.5 1.6 + - - -
209A LYS 2.9 34.9 + - - +
237A LEU* 3.6 7.9 - - - +
239A ARG* 1.3 74.6 - - - +
241A THR* 1.3 63.8 + - - -
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Residues in contact with THR 241 (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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146A ILE 3.8 0.9 - - - +
147A THR* 3.3 3.8 - - - +
148A ASP* 2.9 38.1 + - - +
152A GLY* 3.7 6.8 - - - -
153A MET* 4.1 5.5 - - + +
206A VAL* 3.8 22.4 - - + -
207A TYR 3.3 11.9 - - - +
208A THR* 3.2 15.4 + - - -
237A LEU* 4.2 2.7 - - - +
240A GLY* 1.3 74.9 - - - -
242A ARG* 1.3 61.4 + - - +
243A ILE* 4.0 14.6 - - + -
1001A BC2 3.1 35.1 + - - +
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Residues in contact with ARG 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A SO4 3.0 26.2 + - - -
136A SER* 4.8 3.6 + - - -
143A ILE* 5.5 2.0 - - - +
145A SER* 3.4 21.9 + - - -
146A ILE 3.8 2.7 - - - -
147A THR* 3.5 14.8 + - - +
205A ILE 3.9 0.7 - - - +
206A VAL* 3.3 4.7 - - - +
207A TYR* 2.7 69.2 + - + +
237A LEU* 3.9 17.2 - - + +
241A THR* 1.3 72.6 - - - +
243A ILE* 1.3 65.3 + - - +
244A SER* 2.9 23.7 + - - +
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Residues in contact with ILE 243 (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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103A LEU* 4.4 28.3 - - + +
106A ASN* 5.7 1.3 - - + +
144A LEU 3.7 2.4 - - - +
145A SER* 3.2 3.8 - - - -
146A ILE* 2.8 52.4 + - + +
148A ASP* 5.4 0.2 - - - +
194A PHE* 4.2 5.8 - - + -
204A VAL* 3.8 15.7 - - + -
205A ILE 3.9 1.8 - - - -
206A VAL* 3.8 13.2 - - + -
241A THR* 4.0 8.3 - - + -
242A ARG* 1.3 78.9 - - - +
244A SER* 1.3 59.1 + - - +
245A LEU* 3.7 23.1 - - + -
1001A BC2 3.8 43.3 - - + +
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Residues in contact with SER 244 (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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143A ILE* 4.0 15.7 - - - -
144A LEU 3.6 4.7 - - - -
145A SER* 3.5 4.9 + - - -
204A VAL* 3.4 4.2 - - - +
205A ILE* 2.9 45.1 + - - -
207A TYR* 3.5 13.0 - - - -
242A ARG* 2.9 31.6 + - - +
243A ILE* 1.3 72.3 - - - +
245A LEU* 1.3 61.9 + - - +
246A HIS* 4.2 7.3 + - - -
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Residues in contact with LEU 245 (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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99A PHE* 3.6 36.3 - - + -
103A LEU* 4.0 8.7 - - + -
142A ASN 3.6 0.2 - - - +
143A ILE* 3.2 5.7 - - - -
144A LEU* 2.8 43.5 + - + +
146A ILE* 4.4 6.7 - - + -
197A ALA* 4.1 13.2 - - + -
200A VAL* 4.3 9.4 - - + -
201A ALA* 3.7 11.7 - - + -
203A LYS 3.8 2.9 - - - -
204A VAL* 3.7 21.8 - - + -
243A ILE* 3.7 29.6 - - + -
244A SER* 1.3 71.2 - - - +
246A HIS* 1.3 61.4 + - - +
247A LEU* 3.2 12.3 + - + +
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Residues in contact with HIS 246 (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 LYS 5.0 3.4 - - - +
142A ASN* 3.8 6.5 - - - -
143A ILE* 3.4 33.5 - - + +
201A ALA* 3.5 1.7 - - - -
202A ASP* 3.2 29.9 + - - +
203A LYS* 3.0 42.9 + - + +
205A ILE* 3.5 38.1 - - + +
207A TYR* 5.9 0.7 - - - -
244A SER* 4.4 9.4 + - - -
245A LEU* 1.3 67.6 - - - +
247A LEU* 1.3 66.2 + - - +
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Residues in contact with LEU 247 (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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142A ASN* 3.0 34.4 + - - +
144A LEU* 4.4 16.4 - - + -
200A VAL* 3.4 35.9 - - + +
201A ALA* 4.2 0.2 - - - +
202A ASP* 4.6 2.6 - - - +
245A LEU* 3.4 12.8 - - + +
246A HIS* 1.3 76.0 - - - +
248A LYS* 1.3 67.9 + - - +
249A GLU 3.9 0.5 + - - -
251A ALA 3.5 18.8 - - - +
254A LEU* 3.9 22.0 - - + -
255A LEU* 3.8 36.3 - - + -
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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