Contacts of the strand formed by residues 289 - 300 (chain C) in PDB entry 6RQT
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 VAL 289 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233C ILE* 5.6 2.9 - - + -
234C ASN 3.3 14.1 - - - +
235C ILE* 3.7 14.6 - - + +
239C ILE* 4.8 8.7 - - + -
247C PHE* 3.6 41.3 - - + -
279C VAL* 5.0 9.6 - - + -
280C LEU* 5.6 4.7 - - - +
285C PHE* 3.4 36.9 + - + +
286C ALA 4.0 7.3 - - - +
288C LYS* 1.3 86.0 - - + +
290C LYS* 1.3 72.0 + - - +
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Residues in contact with LYS 290 (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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233C ILE* 3.5 6.5 - - - +
234C ASN* 2.7 52.1 + - + +
235C ILE 5.3 1.3 - - - -
236C LEU* 3.4 32.6 - - - +
280C LEU* 6.1 1.6 - - - -
286C ALA 4.9 2.9 - - - +
287C ASP* 2.6 38.7 + - - +
288C LYS 4.2 1.2 - - - -
289C VAL* 1.3 78.4 - - - +
291C LEU* 1.3 65.9 + - - +
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Residues in contact with LEU 291 (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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232C GLN 3.5 7.0 - - - +
233C ILE* 3.7 22.7 - - + -
234C ASN* 4.0 4.9 - - - +
251C PHE* 5.2 2.0 - - + -
275C VAL* 5.5 6.7 - - + -
277C ARG* 3.5 56.5 - - + +
279C VAL* 4.5 7.0 - - + -
280C LEU* 3.7 29.2 - - + -
290C LYS* 1.3 79.8 - - - +
292C GLY* 1.3 64.0 + - - +
293C ARG* 5.5 1.3 - - - +
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Residues in contact with GLY 292 (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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231C PRO* 3.6 1.6 - - - +
232C GLN* 2.5 48.1 + - - +
234C ASN* 4.2 1.3 - - - +
291C LEU* 1.3 76.9 - - - +
293C ARG* 1.3 69.6 + - - -
295C ARG* 5.7 1.3 - - - -
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Residues in contact with ARG 293 (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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940B GLU* 6.0 0.6 - - - +
1012B PRO* 3.7 18.2 - - - +
1014B TYR* 3.9 29.9 + - - -
1021B GLU* 3.3 26.4 + - - +
1025B ASP* 4.5 1.0 + - - -
228C ARG* 6.0 1.0 - - - +
229C LEU* 3.7 25.0 + - + +
230C LEU 3.6 6.5 - - - +
231C PRO* 4.1 8.2 - - - +
232C GLN* 3.7 6.8 - - - +
275C VAL* 3.3 46.0 - - - +
277C ARG* 3.4 26.1 - - - +
291C LEU* 5.5 0.4 - - - +
292C GLY* 1.3 83.6 + - - -
294C VAL* 1.3 60.7 + - - +
295C ARG* 3.0 32.2 + - - +
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Residues in contact with VAL 294 (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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229C LEU* 3.4 12.1 - - - +
230C LEU* 3.0 27.5 + - + +
232C GLN* 3.6 27.5 - - + +
293C ARG* 1.3 70.7 - - - +
295C ARG* 1.3 59.4 + - - +
296C ASN* 3.2 20.6 + - + +
297C HIS* 3.7 33.4 + - + +
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Residues in contact with ARG 295 (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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1021B GLU* 3.4 28.0 + - - +
59C ILE 3.8 9.4 - - - +
60C ASP* 5.0 5.2 - - - +
61C THR* 5.0 11.8 - - + +
229C LEU* 3.7 15.7 - - + -
292C GLY* 5.7 0.8 - - - -
293C ARG* 3.0 35.0 + - - +
294C VAL* 1.3 71.3 - - - +
296C ASN* 1.3 58.5 + - - +
297C HIS 3.7 0.9 - - - -
298C PHE* 4.4 9.8 - - - -
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Residues in contact with ASN 296 (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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39C ASP* 4.2 6.5 + - - -
57C ILE* 3.3 4.3 - - - +
58C ASN* 2.6 61.5 + - - +
59C ILE 2.8 35.4 + - - +
60C ASP* 4.9 0.2 - - - -
294C VAL* 3.1 10.0 - - + +
295C ARG* 1.3 80.4 - - - +
297C HIS* 1.3 56.8 + - - +
298C PHE* 4.2 3.1 - - - -
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Residues in contact with HIS 297 (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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41C GLU* 5.6 0.4 - - - -
43C ASN* 6.2 0.2 + - - -
55C ASP* 4.7 8.6 - - - +
57C ILE* 3.5 37.6 - - + +
229C LEU* 3.8 0.2 - - - -
230C LEU* 3.0 65.8 + - + +
271C ARG* 6.0 1.6 - - + -
294C VAL* 3.7 21.9 + - + +
295C ARG 3.7 0.6 - - - -
296C ASN* 1.3 78.6 - - - +
298C PHE* 1.3 67.5 + - - +
299C ILE* 4.7 12.0 - - + +
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Residues in contact with PHE 298 (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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54C PHE 3.2 1.1 - - - +
55C ASP* 3.3 5.9 - - - -
56C LEU 3.1 37.2 + - - +
57C ILE* 3.5 4.5 - - - +
59C ILE* 3.6 42.6 - - + -
60C ASP 4.1 2.0 - - - -
61C THR* 3.9 24.7 - - + -
64C ALA* 3.6 26.9 - - + -
227C TYR* 5.0 4.5 - + + -
228C ARG 4.0 3.8 - - - +
229C LEU* 3.5 37.9 - - + -
295C ARG 4.4 5.6 - - - -
297C HIS* 1.3 90.2 - - - +
299C ILE* 1.3 63.8 + - - +
300C PHE* 3.8 22.4 - + + -
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Residues in contact with ILE 299 (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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53C ASN* 4.1 16.2 - - - +
54C PHE 3.3 4.0 - - - -
55C ASP* 3.2 22.9 - - - +
227C TYR* 4.1 0.5 - - - +
228C ARG* 3.2 76.8 + - + +
229C LEU 4.7 2.9 - - - +
230C LEU* 5.7 4.3 - - + +
271C ARG* 4.8 18.6 - - + -
297C HIS* 4.7 12.6 - - + +
298C PHE* 1.3 74.4 - - - +
300C PHE* 1.3 69.4 + - - +
301C ASN* 3.7 19.2 - - - +
174N GLY* 5.0 1.1 - - - -
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Residues in contact with PHE 300 (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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52C ALA 4.0 2.7 - - - +
53C ASN* 3.5 5.0 - - - +
54C PHE* 3.1 58.8 + + + +
56C LEU* 4.1 29.8 - - + -
64C ALA* 5.9 0.7 - - - -
67C PHE* 4.9 9.2 - - + -
71C MET* 5.9 7.9 - - + -
226C SER 4.6 0.4 - - - -
227C TYR* 3.3 59.2 - + + -
298C PHE* 3.8 24.2 - + + -
299C ILE* 1.3 82.7 - - - +
301C ASN* 1.3 78.8 + - - +
302C VAL* 4.9 12.8 - - + -
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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