Contacts of the strand formed by residues 219 - 224 (chain F) in PDB entry 4GK1
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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214F ALA* 4.4 0.9 - - - +
215F SER 4.2 12.8 + - - -
218F GLY* 1.3 75.4 - - - -
220F TRP* 1.3 63.5 + - - +
221F ILE* 3.5 0.3 + - - +
261F MET* 3.3 0.9 - - - -
262F MET* 2.8 49.8 + - - +
277F LEU* 4.1 6.9 - - - +
279F ALA* 3.1 29.1 - - - +
280F TRP* 3.4 7.9 - - - -
281F VAL* 4.1 14.3 - - - +
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Residues in contact with TRP 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182F LYS* 2.9 27.4 + - + -
184F TRP* 3.4 32.4 - + + +
187F ALA* 3.8 29.4 - - + -
198F LEU* 4.0 5.0 - - + +
219F SER* 1.3 73.3 - - - +
221F ILE* 1.3 61.8 + - - +
259F CYS* 3.8 31.0 - - + -
260F VAL 3.4 19.3 - - - -
261F MET* 4.0 6.7 - - + -
271F ALA* 3.9 11.0 - - + -
272F PHE 3.5 20.9 - - - -
273F CYS 4.0 8.7 - - - -
275F ARG* 3.2 22.7 - - + -
277F LEU* 3.3 32.9 - - + +
279F ALA 3.1 13.2 + - - -
280F TRP* 3.6 2.9 - - + -
281F VAL 3.1 25.5 + - - -
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Residues in contact with ILE 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184F TRP* 2.9 23.8 + - - -
198F LEU* 4.1 6.1 - - - -
199F VAL* 3.6 27.4 - - + +
201F ILE* 4.2 4.0 - - + -
219F SER 3.5 0.6 + - - +
220F TRP* 1.3 79.0 - - - +
222F GLY* 1.3 59.2 + - - +
223F LEU 3.1 5.1 + - - +
234F TRP* 3.8 25.8 - - + -
260F VAL* 3.2 44.2 + - + +
261F MET* 4.6 0.7 - - - +
262F MET* 4.0 33.7 - - + -
268F TRP* 4.2 21.1 - - + +
281F VAL* 4.8 0.9 - - + -
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Residues in contact with GLY 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F TRP* 4.5 1.6 - - - -
198F LEU* 3.4 25.0 - - - +
199F VAL 2.8 21.1 + - - -
221F ILE* 1.3 68.7 - - - +
223F LEU* 1.3 56.3 + - - +
234F TRP* 3.2 10.7 - - - -
235F VAL* 2.7 43.4 + - - +
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Residues in contact with LEU 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F TRP* 4.1 1.4 + - - -
221F ILE* 3.1 6.5 + - + +
222F GLY* 1.3 76.7 - - - +
224F ARG* 1.3 63.9 + - - +
232F PHE* 3.7 10.8 - - + -
233F ILE 3.4 35.2 - - - +
234F TRP* 3.4 25.4 - - + +
240F VAL* 3.7 18.6 - - + -
245F TRP* 4.1 8.1 - - + -
259F CYS* 3.9 0.3 - - - -
260F VAL* 3.0 51.8 + - + +
268F TRP* 3.9 33.7 - - + -
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Residues in contact with ARG 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184F TRP* 3.6 34.5 - - + -
188F ARG* 3.8 20.6 - - - +
223F LEU* 1.3 79.1 - - - +
225F ASN* 1.3 61.6 + - - +
226F LEU* 3.5 21.0 + - + +
228F LEU* 3.4 24.7 - - + +
232F PHE* 3.7 8.5 - - - -
233F ILE* 2.8 57.1 + - - +
234F TRP 3.2 21.4 + - - -
235F VAL* 3.5 13.3 + - - +
258F ASP 3.1 15.5 - - - +
259F CYS* 4.2 7.2 - - - -
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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