Contacts of the strand formed by residues 219 - 225 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214E ALA* 4.1 7.3 - - - +
215E SER 4.0 16.3 + - - -
218E GLY* 1.3 78.3 + - - -
220E TRP* 1.3 62.4 + - - +
261E MET* 3.2 0.9 - - - +
262E MET* 2.6 47.9 + - - +
277E LEU* 4.0 7.0 - - - +
279E ALA* 3.1 23.6 - - - +
280E TRP* 4.0 6.7 - - - -
281E VAL* 4.1 15.9 - - - +
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Residues in contact with TRP 220 (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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182E LYS 2.9 26.9 + - - -
184E TRP* 3.4 34.1 - + + +
187E ALA* 3.9 22.4 - - + -
198E LEU* 4.2 4.6 - - + +
219E SER* 1.3 74.4 - - - +
221E ILE* 1.3 62.2 + - - +
259E CYS* 3.6 31.9 - - + -
260E VAL 3.4 13.9 - - - -
261E MET* 4.0 9.2 - - + -
271E ALA* 4.2 10.5 - - + -
272E PHE 3.6 20.4 - - - -
273E CYS 4.2 0.2 - - - -
275E ARG* 3.3 24.0 - - + -
277E LEU* 3.4 30.1 - - + +
279E ALA 3.0 12.2 + - - -
280E TRP* 4.0 13.0 - + + +
281E VAL 3.3 22.7 + - - -
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Residues in contact with ILE 221 (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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184E TRP* 3.0 23.0 + - - -
198E LEU* 4.0 6.5 - - - -
199E VAL* 3.5 26.0 - - + +
201E ILE* 4.0 10.8 - - + -
219E SER 3.5 0.6 + - - +
220E TRP* 1.3 79.1 - - - +
222E GLY* 1.3 60.0 + - - +
223E LEU* 3.0 7.4 + - + +
234E TRP* 3.9 25.8 - - + -
260E VAL* 3.1 42.2 + - + +
261E MET* 4.6 1.3 - - - +
262E MET* 3.9 34.1 - - + -
268E TRP* 4.3 15.5 - - + +
281E VAL* 5.2 0.7 - - + -
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Residues in contact with GLY 222 (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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184E TRP* 4.7 1.1 - - - -
198E LEU* 3.4 27.9 - - - +
199E VAL 2.8 20.6 + - - -
221E ILE* 1.3 68.7 - - - +
223E LEU* 1.3 57.8 + - - +
234E TRP* 3.2 11.5 - - - -
235E VAL* 2.8 40.7 + - - +
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Residues in contact with LEU 223 (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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184E TRP* 4.3 1.9 + - - -
221E ILE* 3.0 7.9 + - + +
222E GLY* 1.3 77.9 - - - +
224E ARG* 1.3 60.9 + - - +
232E PHE* 3.7 12.1 - - + -
233E ILE 3.4 25.6 - - - +
234E TRP* 3.5 26.9 - - + +
240E VAL* 3.6 23.1 - - + -
245E TRP* 4.0 13.2 - - + -
259E CYS* 3.9 0.5 - - - -
260E VAL* 2.9 54.5 + - + +
268E TRP* 3.9 29.8 - - + -
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Residues in contact with ARG 224 (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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228C LEU* 3.2 27.1 - - - +
255C GLN* 5.5 0.6 - - - +
256C GLY* 4.3 4.4 - - - -
258C ASP* 3.2 16.2 + - - -
303C SO4 2.8 43.4 + - - -
184E TRP* 4.0 30.7 - - + -
188E ARG* 4.3 5.2 - - - +
223E LEU* 1.3 77.7 - - - +
225E ASN* 1.3 64.7 + - - +
226E LEU* 3.3 26.2 - - + +
232E PHE* 3.2 7.6 - - - -
233E ILE* 2.8 51.9 + - + +
235E VAL* 5.3 6.1 - - + +
258E ASP* 3.1 13.0 - - + +
259E CYS* 4.6 4.9 - - - -
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Residues in contact with ASN 225 (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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224E ARG* 1.3 77.8 + - - +
226E LEU* 1.3 62.4 + - - +
227E ASP* 3.3 15.3 + - - -
230E GLY* 4.1 3.0 - - - -
231E GLU* 3.1 35.5 + - - +
232E PHE* 3.5 27.4 - - + +
253E ARG* 3.0 16.8 + - - +
258E ASP* 2.8 37.4 + - - +
302E GOL 2.9 24.4 + - - -
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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