Contacts of the strand formed by residues 217 - 222 (chain A) in PDB entry 5GJE
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 217 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A PRO* 5.4 2.2 - - + -
213A LEU* 3.2 6.0 - - - +
214A PHE* 3.1 41.6 + - + +
215A GLU* 2.9 14.9 + - + +
216A ASP* 1.3 81.6 - - + +
218A LEU* 1.3 62.7 + - - +
219A TYR* 3.2 40.3 - - + +
230A ALA* 3.9 18.2 - - + -
231A CYS 3.6 7.9 - - - +
233A LYS* 4.7 0.4 - - - +
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Residues in contact with LEU 218 (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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178A TYR* 3.6 36.3 - - + -
187A ILE* 3.9 37.2 - - + -
200A VAL* 4.0 20.2 - - + -
211A LEU* 4.2 13.5 - - + -
212A THR 3.8 6.3 - - - +
213A LEU* 3.9 15.7 - - + -
216A ASP 4.0 0.2 + - - -
217A ILE* 1.3 70.8 - - - +
219A TYR* 1.3 61.5 + - - +
220A TRP* 3.7 4.1 - - + -
230A ALA* 2.8 26.0 - - - -
231A CYS* 3.2 16.5 + - - +
232A ASN 4.0 9.4 - - - +
233A LYS* 4.2 7.9 - - + +
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Residues in contact with TYR 219 (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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2A PRO* 3.3 24.9 - - + +
4A LEU* 3.7 24.7 - - + -
16A ASP* 4.7 4.7 - - - -
19A ASN* 5.5 0.9 - - - -
211A LEU* 2.9 20.3 - - - +
212A THR* 3.0 38.8 + - + -
213A LEU* 3.9 2.2 - - - -
214A PHE* 3.6 20.8 + - + -
217A ILE* 3.2 54.2 - - + +
218A LEU* 1.3 74.1 - - - +
220A TRP* 1.3 61.3 + - - +
228A ILE* 4.6 1.8 - - + -
229A LEU 3.2 7.0 - - - +
230A ALA* 4.0 8.7 - - + -
242A ILE* 3.4 32.3 - - + -
252A ILE* 5.1 0.7 - - + -
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Residues in contact with TRP 220 (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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187A ILE* 3.9 26.9 - - + -
201A VAL* 5.3 0.4 - - + -
206A PRO* 4.1 22.4 - - + -
207A HIS 4.7 2.8 - - - +
208A PRO* 3.4 26.8 - - + +
210A ALA 3.0 16.2 - - - +
211A LEU* 3.8 10.1 - - + -
218A LEU 3.7 19.7 - - - -
219A TYR* 1.3 80.0 - - - +
221A THR* 1.3 80.4 + - - +
222A ASP* 4.2 2.2 - - - +
228A ILE* 3.2 8.6 - - - +
229A LEU* 2.9 68.2 + - + +
230A ALA 3.9 6.1 - - - -
231A CYS* 4.0 14.8 - - - -
239A LEU* 3.6 26.2 - - + -
252A ILE* 4.8 4.2 - - - +
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Residues in contact with THR 221 (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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6A TYR* 5.4 1.6 - - + -
208A PRO* 3.1 6.6 - - - +
209A PHE* 2.5 35.5 + - - +
210A ALA* 3.1 18.3 + - - +
220A TRP* 1.3 80.9 - - - +
222A ASP* 1.3 59.1 + - - +
223A TRP 3.9 0.4 - - - -
227A SER 3.6 5.8 - - - +
228A ILE* 4.4 9.9 - - + -
249A PRO* 3.5 37.9 - - + -
250A MET 3.1 23.3 + - - +
252A ILE* 4.4 16.8 - - + -
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Residues in contact with ASP 222 (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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205A LEU 5.3 1.0 - - - +
207A HIS* 3.4 41.2 + - - +
209A PHE 4.7 0.2 - - - +
220A TRP* 4.6 1.1 - - - +
221A THR* 1.3 73.6 - - - +
223A TRP* 1.3 64.9 + - - +
224A SER* 2.9 28.6 + - - -
225A THR* 3.1 31.5 + - - +
226A HIS 2.9 16.8 + - - -
227A SER 3.2 11.1 + - - -
229A LEU* 3.9 17.8 - - + +
249A PRO* 5.0 0.2 - - - -
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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