Contacts of the strand formed by residues 320 - 330 (chain C) in PDB entry 4RQE
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 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A TYR* 3.9 10.6 + - - +
225A THR 3.9 1.6 - - - +
226A PRO* 3.5 27.9 - - - +
227A PHE* 3.0 44.8 + - + +
228A PHE* 4.5 18.2 - - + -
189C ALA* 5.3 2.8 - - - +
193C GLY* 5.6 1.4 - - - -
194C TYR* 2.8 49.2 + - + +
300C CYS 3.5 4.5 - - - -
301C PHE* 4.1 18.4 - - + -
318C VAL* 3.5 5.5 - - - +
319C HIS* 1.3 82.4 - - - +
321C PHE* 1.3 65.2 + - - +
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Residues in contact with PHE 321 (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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194C TYR* 3.9 4.9 - - - -
299C THR* 3.3 3.1 - - - +
300C CYS* 2.5 61.7 + - + -
302C ARG* 4.4 16.4 - - + -
318C VAL* 4.3 11.2 - - + -
319C HIS 4.8 0.7 - - - -
320C GLN* 1.3 86.3 - - - +
322C GLU* 1.3 78.0 + - - +
323C LYS* 3.5 33.4 - - + -
432C ALA* 4.9 3.1 - - + -
433C THR 5.3 0.2 - - - -
434C THR* 3.3 24.0 - - - +
602C ANP 3.7 51.6 - + - -
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Residues in contact with GLU 322 (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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224A TYR* 2.6 47.2 + - - -
227A PHE* 3.7 3.8 - - - -
299A THR* 5.0 0.5 + - - -
194C TYR* 4.8 0.5 + - - -
204C GLU* 3.4 16.6 - - - +
208C ILE* 4.5 10.5 - - + -
297C LEU* 5.2 8.1 - - + -
298C SER 3.8 5.4 - - - +
299C THR* 3.2 27.0 + - - +
321C PHE* 1.3 78.9 - - - +
323C LYS* 1.3 65.0 + - - +
433C THR* 2.7 47.4 + - + +
434C THR* 5.3 0.3 + - - -
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Residues in contact with LYS 323 (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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270C ALA 4.5 2.2 - - - -
271C THR* 3.4 29.3 - - - +
272C SER* 3.6 8.2 + - - +
296C GLY 3.6 8.1 - - - +
297C LEU* 5.3 0.8 - - - +
298C SER* 3.0 21.3 + - - +
300C CYS* 3.5 22.1 - - - -
302C ARG* 5.1 1.6 - - - +
321C PHE* 3.5 25.8 - - + -
322C GLU* 1.3 77.3 - - - +
324C ILE* 1.3 63.9 + - - +
325C GLU* 3.4 25.3 + - - +
429C THR* 3.5 28.4 + - + +
431C CYS 3.3 15.3 - - - +
432C ALA* 3.8 7.2 - - - -
433C THR* 4.3 1.3 - - - +
601C SER* 4.6 1.6 - - - -
602C ANP 4.3 13.5 - - - +
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Residues in contact with ILE 324 (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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208C ILE* 3.6 37.0 - - + +
211C ALA* 4.5 12.8 - - + -
212C LEU* 4.3 21.8 - - + -
215C LEU* 3.9 27.4 - - + -
295C ALA 4.8 1.6 - - - -
296C GLY 3.4 11.4 - - - +
297C LEU* 4.1 20.2 - - + +
323C LYS* 1.3 73.2 - - - +
325C GLU* 1.3 58.3 + - - +
429C THR* 3.5 5.2 - - - +
430C MET* 2.8 32.6 + - + -
431C CYS* 2.9 24.7 + - + +
433C THR* 3.9 13.2 - - + -
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Residues in contact with GLU 325 (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 LEU* 5.3 0.2 - - - -
271C THR* 3.6 8.5 - - - -
272C SER* 3.4 7.7 - - - -
273C GLU* 2.7 44.7 + - - +
276C ILE* 4.4 4.2 - - - +
295C ALA* 3.5 4.1 - - - -
296C GLY 2.8 37.1 + - - +
323C LYS* 3.4 13.7 - - - +
324C ILE* 1.3 76.2 - - - +
326C GLN* 1.3 74.9 + - - +
327C PHE* 3.7 2.4 + - - +
427C ASN* 3.3 13.0 - - - +
428C ALA 3.4 15.0 - - - +
429C THR* 3.9 2.9 - - - +
430C MET* 3.6 5.2 - - - +
601C SER* 3.3 19.6 - - - -
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Residues in contact with GLN 326 (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 LEU* 4.0 18.1 - - + +
220C TYR* 4.1 10.1 + - + -
294C TYR 3.6 5.2 - - - -
295C ALA* 4.9 0.7 - - - +
325C GLU* 1.3 77.3 - - - +
327C PHE* 1.3 58.4 + - - +
328C VAL 4.3 0.4 - - - -
344C MET* 3.6 46.2 + - - +
345C ILE* 5.8 0.2 - - - -
347C THR* 4.0 12.9 - - - -
348C ALA* 4.3 7.4 - - - +
427C ASN* 3.3 3.9 - - - -
428C ALA* 2.5 60.9 + - - +
429C THR 4.2 3.6 - - - +
430C MET* 3.5 34.8 - - + +
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Residues in contact with PHE 327 (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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273C GLU* 3.5 29.8 - - + -
276C ILE* 3.5 36.1 - - + -
277C ALA* 3.5 25.8 - - + -
293C LYS 3.6 0.3 - - - -
294C TYR* 2.7 46.5 + - + +
325C GLU* 3.7 2.0 + - - +
326C GLN* 1.3 73.6 - - - +
328C VAL* 1.3 60.3 + - - +
329C TYR* 3.6 37.0 - + - -
398C CYS* 6.4 0.7 - - - -
402C GLN* 5.0 4.7 - - - -
425C MET* 4.7 15.3 - - + -
426C LEU 3.3 21.8 - - - -
427C ASN* 3.5 19.5 - - + -
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Residues in contact with VAL 328 (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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220C TYR* 4.0 23.1 - - + +
291C PRO 5.3 0.2 - - - -
292C ILE 3.4 9.4 - - - +
293C LYS* 4.2 10.5 - - + -
327C PHE* 1.3 80.4 - - - +
329C TYR* 1.3 77.7 + - - +
330C SER* 3.9 3.1 + - - -
340C MET* 3.9 33.0 - - + -
344C MET* 3.7 27.1 - - - -
425C MET* 3.9 0.9 - - - -
426C LEU* 3.2 42.5 + - + +
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Residues in contact with TYR 329 (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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276C ILE 2.5 26.7 + - - -
277C ALA* 3.1 14.4 + - - -
280C HIS* 4.0 21.1 + + + +
285C LEU* 4.4 18.4 - - + -
290C LEU* 3.0 18.3 - - + +
291C PRO 3.8 0.9 - - - -
292C ILE* 2.9 34.7 + - + +
294C TYR* 3.6 35.4 - + - -
327C PHE* 3.6 22.0 - + - -
328C VAL* 1.3 78.2 - - - +
330C SER* 1.3 61.4 + - - +
408C ILE* 4.0 11.0 - - + -
423C VAL* 4.8 6.5 - - + -
424C HIS 4.1 3.4 - - - -
425C MET* 3.4 30.5 - - + +
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Residues in contact with SER 330 (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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290C LEU* 4.0 13.2 - - - +
291C PRO* 4.9 0.9 - - - -
328C VAL* 4.5 9.9 - - - -
329C TYR* 1.3 75.7 - - - +
331C SER* 1.3 62.0 + - - +
336C LYS 5.3 1.1 - - - -
337C SER* 3.9 21.0 - - - -
340C MET* 4.8 15.0 - - - -
423C VAL* 3.6 10.3 - - - +
424C HIS* 3.2 38.3 + - - +
426C LEU* 3.6 14.6 - - - +
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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