Contacts of the strand formed by residues 219 - 225 (chain C) in PDB entry 4GJ0
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 SER 219 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214C ALA* 5.0 0.7 - - - +
215C SER* 3.9 16.6 + - - -
218C GLY* 1.3 74.6 - - - -
220C TRP* 1.3 67.0 + - - +
261C MET* 3.2 2.8 - - - -
262C MET* 2.7 51.9 + - - +
277C LEU* 4.0 6.4 - - - +
279C ALA* 3.4 18.2 - - - +
280C TRP 4.0 9.1 + - - -
281C VAL* 4.1 18.3 - - - +
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Residues in contact with TRP 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C LYS* 2.9 29.2 + - + -
183C GLN 4.0 0.9 - - - -
184C TRP* 3.4 41.7 - + + +
187C ALA* 4.0 13.7 - - + -
198C LEU* 4.2 4.5 - - + +
219C SER* 1.3 73.6 - - - +
221C ILE* 1.3 61.4 + - - +
259C CYS* 3.5 23.6 - - + -
260C VAL 3.3 28.0 - - - -
261C MET* 4.2 2.2 - - + -
271C ALA* 3.8 17.3 - - + -
272C PHE 3.5 23.1 - - - -
273C CYS* 3.9 1.8 - - - -
275C ARG* 3.2 22.4 + - + -
277C LEU* 3.6 31.3 - - + +
279C ALA 3.1 12.7 + - - -
280C TRP* 3.6 10.8 - - + +
281C VAL 3.3 23.7 + - - -
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Residues in contact with ILE 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TRP* 2.9 24.6 + - - -
198C LEU* 4.1 6.7 - - - +
199C VAL* 3.5 26.5 - - + +
201C ILE* 4.1 10.8 - - + -
219C SER* 4.2 0.7 - - - +
220C TRP* 1.3 78.3 - - - +
222C GLY* 1.3 59.2 + - - +
223C LEU* 3.3 7.0 + - + +
234C TRP* 3.9 22.9 - - + -
260C VAL* 3.4 40.0 + - + +
261C MET* 4.7 1.1 - - - -
262C MET* 3.8 33.4 - - + -
268C TRP* 4.2 17.0 - - + +
281C VAL* 5.1 0.9 - - + -
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Residues in contact with GLY 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TRP* 4.4 3.0 - - - -
198C LEU* 3.5 22.4 - - - +
199C VAL 3.0 18.6 + - - -
221C ILE* 1.3 74.9 - - - +
223C LEU* 1.3 59.2 + - - +
224C ARG* 3.8 1.2 + - - +
233C ILE 3.9 0.2 - - - +
234C TRP* 3.5 7.6 - - - -
235C VAL* 2.9 39.4 + - - +
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Residues in contact with LEU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TRP* 4.6 1.0 + - - -
221C ILE* 3.3 5.9 - - + +
222C GLY* 1.3 78.5 - - - +
224C ARG* 1.3 63.3 + - - +
232C PHE* 3.7 6.3 - - + -
233C ILE 3.5 36.1 - - - +
234C TRP* 3.5 24.8 - - + +
240C VAL* 3.7 22.7 - - + -
245C TRP* 3.8 34.3 - - + -
260C VAL* 3.4 36.9 + - + +
268C TRP* 4.0 21.8 - - + -
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Residues in contact with ARG 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PHE* 3.5 34.4 - - + -
274A ASP* 2.9 42.6 + - - -
184C TRP* 3.3 42.7 - - + -
188C ARG* 3.5 14.1 - - - +
222C GLY 3.8 0.4 + - - +
223C LEU* 1.3 78.7 - - - +
225C ASN* 1.3 62.7 + - - +
226C LEU* 3.6 25.5 + - + +
231C GLU 3.5 0.2 - - - +
232C PHE* 3.3 8.7 - - - -
233C ILE 2.9 37.6 + - - +
234C TRP 5.3 1.2 + - - -
235C VAL* 4.5 16.0 + - - +
258C ASP 3.4 11.4 - - - +
259C CYS* 4.2 5.8 - - - +
260C VAL* 4.8 0.7 - - - -
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Residues in contact with ASN 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A GLU* 5.0 1.0 - - - +
272A PHE* 3.7 12.1 - - - -
224C ARG* 1.3 71.2 - - - +
226C LEU* 1.3 58.8 + - - +
227C ASP 2.8 25.0 + - - +
228C LEU* 4.7 3.0 + - - +
230C GLY* 3.4 1.4 - - - -
231C GLU 2.8 33.3 + - - -
232C PHE* 3.6 30.1 - - + -
253C ARG* 3.6 18.1 - - - +
258C ASP* 2.9 56.7 + - + +
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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