Contacts of the strand formed by residues 226 - 238 (chain C) in PDB entry 4LL4
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 GLN 226 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A ARG 3.8 5.7 - - - +
72A TYR* 3.4 33.0 - - - -
73A GLU* 2.8 50.6 + - - +
74A ASP* 5.8 0.2 + - - -
225A GLY* 3.8 10.8 - - - -
222C LEU* 3.2 5.9 - - - -
223C ALA 2.3 50.9 + - - +
224C ASN 3.8 6.1 - - - +
225C GLY* 1.3 87.6 - - - +
227C THR* 1.3 69.4 + - - +
228C LYS* 3.7 14.3 - - + +
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Residues in contact with THR 227 (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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225A GLY* 4.6 5.6 + - - -
106C PRO* 5.7 10.5 - - + +
220C THR* 3.3 32.1 - - + -
221C TYR 3.4 5.4 - - - +
222C LEU* 3.9 17.0 - - + +
226C GLN* 1.3 81.4 + - - +
228C LYS* 1.3 59.4 + - - +
229C VAL* 6.0 0.7 - - + -
270C LEU* 5.4 4.0 - - + -
271C ARG* 5.5 2.5 - - - +
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Residues in contact with LYS 228 (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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73A GLU* 3.0 54.4 + - - +
74A ASP* 4.1 12.3 - - - +
75A THR* 5.6 1.8 + - - +
220C THR* 3.5 7.1 - - - +
221C TYR* 2.8 60.0 + - + +
223C ALA* 3.5 27.6 - - + -
224C ASN 5.7 0.9 - - - -
226C GLN* 3.8 22.0 - - + +
227C THR* 1.3 78.3 - - - +
229C VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 229 (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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74A ASP* 5.2 7.3 + - - +
75A THR* 5.8 1.4 - - - +
77A LEU* 6.2 2.5 - - + -
85A GLU* 3.9 7.6 - - - +
218C ARG* 4.1 20.4 - - + -
219C HIS 3.3 4.0 - - - +
220C THR* 3.8 20.0 - - + +
221C TYR* 4.2 2.2 - - - -
227C THR* 6.0 0.7 - - + -
228C LYS* 1.3 81.5 - - - +
230C LEU* 1.3 59.8 + - - +
231C THR* 3.9 19.2 + - - +
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Residues in contact with LEU 230 (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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85A GLU* 3.3 30.5 - - + +
218C ARG* 3.5 0.3 - - - -
219C HIS* 2.7 63.0 + - + +
221C TYR* 3.9 16.8 - - + +
229C VAL* 1.3 72.8 - - - +
231C THR* 1.3 73.3 + - - +
232C GLN* 5.1 10.8 - - + +
265C LEU* 4.2 19.1 - - + +
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Residues in contact with THR 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 4.6 18.5 - - + +
82A PRO 4.5 4.9 - - - +
84A GLY* 3.7 17.7 - - - +
85A GLU* 3.2 32.6 + - - +
86A ASN* 4.4 0.5 + - - +
216C VAL* 3.7 24.0 - - + -
217C ALA 3.3 4.7 - - - +
218C ARG* 3.5 20.5 - - + +
229C VAL* 3.9 9.7 + - - +
230C LEU* 1.3 83.4 - - - +
232C GLN* 1.3 65.9 + - - +
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Residues in contact with GLN 232 (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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83A THR 3.8 3.8 - - - -
86A ASN* 3.7 25.8 - - + +
216C VAL* 3.5 2.8 - - - -
217C ALA* 2.8 36.2 + - + +
219C HIS* 3.1 34.7 + - + +
230C LEU* 5.1 11.0 - - + +
231C THR* 1.3 78.2 - - - +
233C LYS* 1.3 62.5 + - - +
234C LEU* 3.6 25.3 + - + +
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Residues in contact with LYS 233 (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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83A THR* 3.2 43.6 + - + +
86A ASN* 3.0 32.7 + - - +
87A GLU* 2.5 41.7 + - + +
214C ALA* 4.4 15.9 - - + -
215C ILE 3.9 3.6 - - - -
216C VAL* 4.0 2.7 - - + -
232C GLN* 1.3 71.9 + - - +
234C LEU* 1.3 63.0 + - - +
235C SER 3.9 6.6 + - - +
236C SER* 3.3 25.8 + - - +
279C TYR* 5.3 3.8 + - - -
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Residues in contact with LEU 234 (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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215C ILE* 2.9 30.2 + - + +
217C ALA* 3.8 28.7 - - + -
219C HIS* 5.7 1.1 - - + +
232C GLN* 3.9 32.5 - - - +
233C LYS* 1.3 74.5 - - - +
235C SER* 1.3 69.1 + - - +
258C GLN* 3.3 32.2 + - - +
274C TYR* 3.9 17.9 - - + -
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Residues in contact with SER 235 (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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214C ALA* 3.2 2.3 - - - +
215C ILE* 2.9 33.6 + - - -
233C LYS* 3.6 5.3 + - - +
234C LEU* 1.3 90.4 - - - +
236C SER* 1.3 62.7 + - - +
255C LEU* 3.2 13.9 - - - +
256C ARG* 3.0 26.3 + - - +
257C VAL* 5.8 0.2 - - - -
258C GLN* 3.9 11.8 + - - -
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Residues in contact with SER 236 (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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213C ALA 2.9 16.8 - - - -
214C ALA* 3.6 12.3 - - - +
233C LYS* 3.3 24.2 + - - -
235C SER* 1.3 78.5 + - - +
237C VAL* 1.3 72.1 + - - +
255C LEU* 4.1 5.9 - - - +
279C TYR* 5.8 1.6 - - - -
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Residues in contact with VAL 237 (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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197C ILE* 5.3 1.1 - - + -
212C LYS* 3.4 7.6 - - - +
213C ALA* 3.0 46.1 + - + +
236C SER* 1.3 83.2 - - - +
238C ARG* 1.3 62.7 + - - +
239C GLY 4.3 0.7 - - - -
250C TRP* 4.5 4.5 - - + -
253C LYS* 4.4 27.8 - - + -
254C SER 4.0 19.5 - - - +
255C LEU* 4.4 16.4 - - + -
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Residues in contact with ARG 238 (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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210C VAL* 4.0 24.5 - - + +
211C PRO 4.0 2.5 - - - -
212C LYS* 4.4 15.1 - - + +
237C VAL* 1.3 79.0 - - - +
239C GLY* 1.3 87.6 + - - +
240C ASN* 4.7 1.2 + - - +
241C HIS* 2.8 43.2 + - - +
250C TRP* 4.7 1.1 - - - -
253C LYS* 4.6 6.5 - - - -
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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