Contacts of the strand formed by residues 251 - 256 (chain I) in PDB entry 3EXG
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 ILE 251 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17I LEU* 4.4 9.9 - - + -
189I CYS 3.2 4.2 + - - -
190I ILE* 3.5 18.0 - - + +
191I PHE* 2.9 24.6 + - - -
220I ILE* 3.7 4.3 - - - -
221I PRO* 3.1 23.6 - - + +
223I LEU* 3.7 22.9 - - + -
239I PHE* 4.1 19.3 - - + -
240I ALA* 4.1 11.4 - - + -
243I TYR* 4.1 20.0 - - + -
244I CYS* 3.8 22.2 - - - -
250I PRO* 1.3 75.3 - - - +
252I LEU* 1.3 66.0 + - - +
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Residues in contact with LEU 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165I TYR* 3.9 15.0 - - - +
179I TYR* 3.6 29.8 - - + +
191I PHE* 3.0 18.4 - - + +
193I CYS* 5.8 2.2 - - + +
213I TYR 3.2 27.4 - - - +
214I TYR* 3.8 21.8 - - - +
216I ARG 4.7 0.2 - - - -
217I GLY* 3.9 21.8 - - - +
220I ILE* 3.8 18.6 - - + +
221I PRO 3.0 10.9 + - - +
222I GLY* 3.3 8.9 - - - -
223I LEU* 3.2 19.5 - - - +
251I ILE* 1.3 75.5 - - - +
253I MET* 1.3 60.8 + - - +
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Residues in contact with MET 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75I LEU* 3.6 31.6 - - + -
162I LEU* 5.7 0.7 - - + -
190I ILE* 4.5 8.3 - - + -
191I PHE 2.8 10.1 + - - +
192I ILE* 3.2 27.9 - - + +
193I CYS* 3.0 22.5 + - - +
223I LEU* 3.5 19.3 - - + +
225I VAL* 4.0 13.5 - - + -
233I VAL 5.2 0.2 - - - +
236I ALA* 4.0 31.9 - - + +
237I THR* 3.8 10.1 - - + +
240I ALA* 4.5 10.1 - - + -
251I ILE* 5.8 0.2 - - + -
252I LEU* 1.3 79.8 - - - +
254I GLU* 1.3 60.9 + - - +
255I LEU* 3.6 17.4 + - + -
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Residues in contact with GLU 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193I CYS* 3.7 13.0 - - + +
195I ASN* 3.4 30.1 + - + -
211I THR 4.1 1.8 - - - +
213I TYR* 3.0 39.9 + - + +
214I TYR* 3.0 28.7 + - + +
223I LEU 2.9 11.2 + - - +
224I ARG* 3.2 28.4 + - - +
225I VAL 2.8 28.8 + - - +
253I MET* 1.3 71.6 - - - +
255I LEU* 1.3 61.8 + - - +
256I GLN* 3.4 8.0 + - + +
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Residues in contact with LEU 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I CYS* 3.6 33.9 - - + -
75I LEU* 4.0 24.7 - - + -
192I ILE* 3.6 22.9 - - + -
193I CYS 3.1 9.3 + - - +
194I GLU* 3.7 12.2 - - + -
195I ASN 2.9 27.2 + - - +
225I VAL* 3.9 22.4 - - + -
227I GLY* 4.7 6.7 - - - -
233I VAL* 4.8 7.0 - - + -
253I MET* 3.6 26.7 + - + -
254I GLU* 1.3 72.4 - - - +
256I GLN* 1.3 62.1 + - - +
257I THR* 3.5 2.8 + - + +
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Residues in contact with GLN 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I LYS* 5.9 3.3 - - - -
195I ASN* 3.4 15.8 - - - +
197I ARG* 3.1 38.0 + - - +
224I ARG* 3.5 39.1 + - - +
225I VAL 3.0 17.5 + - - +
226I ASP* 4.2 7.3 - - + +
227I GLY* 2.6 29.5 + - - +
228I MET* 3.9 2.8 + - - +
254I GLU* 3.4 21.2 + - + +
255I LEU* 1.3 70.1 - - - +
257I THR* 1.3 60.4 + - - +
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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