Contacts of the strand formed by residues 240 - 243 (chain E) in PDB entry 3FZ7
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 MET 240 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E MET* 4.8 3.6 - - - -
140E ARG* 5.0 0.9 + - - -
205E VAL* 3.3 14.8 - - + +
207E PRO* 3.4 26.5 - - + -
220E PRO* 3.6 17.9 - - + +
223E LEU* 3.5 29.6 - - + -
224E HIS* 4.0 20.0 - - - +
227E LEU* 3.8 19.5 - - + -
239E ASP* 1.3 79.0 - - - +
241E HIS* 1.3 60.6 + - - +
242E ILE* 4.2 4.7 - - + -
266E ARG* 2.8 15.3 + - + +
267E VAL* 3.6 25.8 - - + -
268E LYS* 2.9 30.3 + - - +
269E SER* 3.8 2.3 + - - -
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Residues in contact with HIS 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ALA 4.6 1.8 - - - -
130E CYS* 4.9 0.2 - - - -
133E GLY* 3.9 22.1 - - - -
137E MET* 3.9 26.1 - - + -
166E TRP* 3.8 27.1 - + - -
205E VAL 3.0 6.1 + - - -
206E VAL* 3.3 30.7 - - + +
207E PRO* 3.4 1.0 - - - +
240E MET* 1.3 73.2 - - - +
242E ILE* 1.3 74.5 + - - +
269E SER* 2.8 30.8 + - - +
270E ILE 3.9 7.2 - - - -
271E SER* 2.8 39.5 + - - -
287E VAL* 4.2 3.8 - - + -
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Residues in contact with ILE 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207E PRO* 3.7 26.2 - - + +
209E PHE* 3.7 28.5 - - + -
220E PRO* 3.7 29.4 - - + -
240E MET* 4.6 2.9 - - + -
241E HIS* 1.3 74.2 - - - +
243E ASP* 1.3 61.4 + - - +
244E ALA* 3.1 8.7 + - + -
260E TRP* 3.5 29.4 - - + +
267E VAL* 3.9 26.7 - - + -
269E SER 3.0 8.7 + - - -
270E ILE* 3.5 11.7 - - + +
271E SER 3.0 26.7 + - - +
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Residues in contact with ASP 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E SER* 4.8 2.3 + - - -
130E CYS* 4.2 10.7 - - - -
163E GLN* 4.3 13.7 + - - +
165E CYS* 4.5 0.5 - - - -
166E TRP* 3.0 36.2 + - + +
206E VAL* 3.8 6.5 - - + -
207E PRO 3.2 15.2 + - - +
208E THR* 3.6 16.5 + - - +
209E PHE* 2.8 25.9 + - - -
210E GLY 5.4 0.3 - - - +
241E HIS* 3.5 3.8 + - - -
242E ILE* 1.3 70.1 - - - +
244E ALA* 1.3 56.5 + - - +
245E ALA* 3.0 26.9 + - - +
271E SER* 4.2 8.7 + - - +
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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