Contacts of the helix formed by residues 320 - 338 (chain C) in PDB entry 1RR8
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 320 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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318C GLN 4.0 0.4 + - - -
319C MET* 1.3 77.7 - - - +
321C LYS* 1.3 60.4 + - - +
322C GLU* 3.2 24.7 + - - +
323C GLU* 3.3 21.1 + - - +
324C LYS* 3.1 28.8 + - - +
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Residues in contact with LYS 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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320C SER* 1.3 74.6 - - - +
322C GLU* 1.3 68.5 + - - +
323C GLU 3.3 2.9 - - - -
324C LYS* 4.3 6.3 - - - +
325C LEU* 3.3 32.6 - - + +
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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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320C SER* 3.2 19.2 + - - +
321C LYS* 1.3 93.9 + - - +
323C GLU* 1.3 69.2 + - + +
326C LYS* 3.2 25.8 - - - +
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Residues in contact with GLU 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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319C MET* 3.6 34.4 - - + +
320C SER* 3.3 22.8 + - - +
322C GLU* 1.3 90.2 - - + +
324C LYS* 1.3 62.8 + - - +
325C LEU 3.3 1.3 - - - -
326C LYS* 3.9 6.2 - - - +
327C ILE* 3.3 37.2 + - + +
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Residues in contact with LYS 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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17A A 3.7 39.4 + - - +
18A T 4.5 15.6 + - - +
316C ARG 5.0 5.6 + - - -
317C LYS* 4.6 18.5 - - - +
319C MET* 4.5 28.4 - - + +
320C SER 3.1 16.2 + - - +
321C LYS* 4.9 3.1 - - - -
323C GLU* 1.3 77.0 - - - +
325C LEU* 1.3 58.9 + - - +
327C ILE* 5.1 1.2 - - - +
328C LYS* 3.6 28.0 + - - +
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Residues in contact with LEU 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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321C LYS* 3.3 21.9 + - + +
323C GLU 3.3 0.2 - - - -
324C LYS* 1.3 78.0 - - - +
326C LYS* 1.3 66.1 + - - +
328C LYS* 3.5 6.1 + - + +
329C GLU* 3.2 52.5 + - + +
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Residues in contact with LYS 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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322C GLU 3.2 25.3 + - - +
323C GLU* 3.5 9.0 + - - +
324C LYS 3.5 0.4 - - - -
325C LEU* 1.3 77.9 - - - +
327C ILE* 1.3 63.2 + - + +
329C GLU* 3.0 9.5 + - - +
330C GLU* 3.0 62.3 + - + +
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Residues in contact with ILE 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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319C MET* 4.4 24.2 - - + -
323C GLU* 3.3 22.6 + - + +
324C LYS* 5.1 1.1 - - - +
326C LYS* 1.3 83.4 - - + +
328C LYS* 1.3 63.3 + - + +
330C GLU* 3.5 9.8 + - + +
331C ASN* 3.2 38.8 + - - +
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Residues in contact with LYS 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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17A A 3.5 35.3 + - - -
109B T 6.0 0.2 - - - -
110B T 5.1 14.1 + - - -
324C LYS* 3.6 20.9 + - - +
325C LEU* 3.5 8.7 + - + +
326C LYS 3.2 0.4 - - - -
327C ILE* 1.3 84.4 - - + +
329C GLU* 1.3 59.3 + - + +
331C ASN* 3.9 13.2 - - + +
332C GLU* 3.3 29.7 + - - +
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Residues in contact with GLU 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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325C LEU* 3.2 45.3 + - + +
326C LYS* 3.0 9.7 + - - +
328C LYS* 1.3 78.4 - - + +
330C GLU* 1.3 69.0 + - - +
331C ASN 3.2 1.3 - - - -
332C GLU* 3.6 19.5 + - - +
333C LYS* 3.3 20.3 + - - +
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Residues in contact with GLU 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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326C LYS* 3.0 59.8 + - + +
327C ILE* 3.5 9.6 + - + +
329C GLU* 1.3 84.2 - - - +
331C ASN* 1.3 64.7 + - - +
332C GLU 3.3 0.2 - - - -
333C LYS* 3.4 29.6 + - + +
334C LEU* 3.3 22.9 + - - +
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Residues in contact with ASN 331 (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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110B T 4.8 9.2 + - - -
327C ILE* 3.2 30.3 + - - +
328C LYS* 3.9 16.2 - - + +
330C GLU* 1.3 82.0 + - - +
332C GLU* 1.3 57.2 + - + +
334C LEU* 3.6 13.6 + - - +
335C LEU* 3.1 26.5 + - - +
353C PHE* 5.7 0.2 - - - -
354C LYS* 3.8 27.1 + - - +
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Residues in contact with GLU 332 (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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328C LYS 3.3 18.7 + - - +
329C GLU* 3.6 24.1 + - - +
330C GLU 3.3 0.2 - - - -
331C ASN* 1.3 76.1 - - + +
333C LYS* 1.3 62.7 + - - +
334C LEU 3.2 1.6 - - - -
335C LEU* 3.3 7.7 + - + +
336C LYS* 3.2 50.5 + - - +
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Residues in contact with LYS 333 (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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329C GLU 3.3 10.0 + - - +
330C GLU* 3.4 32.9 + - - +
332C GLU* 1.3 77.0 - - - +
334C LEU* 1.3 67.5 + - - +
335C LEU 3.4 0.2 - - - -
336C LYS* 4.0 7.3 - - - +
337C GLU* 3.2 48.2 + - - +
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Residues in contact with LEU 334 (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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226C VAL* 4.2 27.4 - - + -
330C GLU 3.3 15.5 + - - +
331C ASN* 3.6 17.5 - - - +
332C GLU 3.2 0.2 - - - -
333C LYS* 1.3 84.0 - - - +
335C LEU* 1.3 57.5 + - - +
336C LYS 3.3 0.4 - - - -
337C GLU* 4.6 2.9 - - - +
338C TYR* 3.1 55.9 + - + +
353C PHE* 3.7 8.1 - - + -
354C LYS* 3.9 25.8 - - - -
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Residues in contact with LEU 335 (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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331C ASN 3.1 17.6 + - - +
332C GLU* 3.3 9.6 + - + +
334C LEU* 1.3 78.0 - - - +
336C LYS* 1.3 70.8 + - + +
339C GLY* 3.2 24.6 - - - +
340C PHE* 3.6 18.9 - - + -
349C ARG* 4.8 21.1 - - + +
353C PHE* 3.8 30.9 - - + -
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Residues in contact with LYS 336 (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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332C GLU* 3.2 39.0 + - - +
333C LYS* 3.8 6.5 + - - +
334C LEU 3.3 0.2 - - - -
335C LEU* 1.3 94.4 - - + +
337C GLU* 1.3 59.2 + - - +
338C TYR 3.7 0.2 - - - -
340C PHE* 4.0 24.9 - - + +
347C LYS* 5.9 1.6 + - - -
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Residues in contact with GLU 337 (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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223C LYS* 3.6 26.2 - - + +
333C LYS* 3.2 40.1 + - - +
334C LEU* 3.5 0.9 + - - +
336C LYS* 1.3 79.2 - - - +
338C TYR* 1.3 84.3 + - + +
339C GLY 3.8 0.2 - - - -
340C PHE 5.1 3.9 - - - +
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Residues in contact with TYR 338 (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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223C LYS* 3.4 43.1 + - + -
224C GLY 3.7 14.5 - - - +
225C PRO 4.6 6.1 - - - -
226C VAL* 3.6 31.0 - - + -
334C LEU* 3.1 28.5 + - + +
337C GLU* 1.3 102.8 + - + +
339C GLY* 1.3 58.4 + - - +
340C PHE 3.3 7.6 - - - -
350C ILE* 3.4 20.0 - - - +
353C PHE* 3.7 15.2 - - + +
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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