Contacts of the helix formed by residues 320 - 334 (chain C) in PDB entry 4R0C
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C ARG* 3.6 15.3 + - - +
319C ASN* 1.3 75.3 - - - +
321C GLY* 1.3 64.9 + - - +
323C VAL* 3.0 26.3 + - - +
324C ILE* 3.6 6.9 + - - +
805C LMT 4.2 19.9 - - - -
23D LEU* 4.0 25.3 - - - +
27D TRP* 5.4 4.5 - - - -
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Residues in contact with GLY 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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319C ASN* 3.3 11.7 + - - +
320C SER* 1.3 78.5 - - - +
322C ALA* 1.3 57.9 + - - +
324C ILE* 3.2 14.9 + - - +
325C THR* 3.0 31.1 + - - -
20D HIS* 4.6 16.1 - - - -
23D LEU* 4.7 5.1 - - - +
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Residues in contact with ALA 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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316C GLN 5.1 0.9 - - - +
317C PHE* 3.5 39.8 - - + -
318C ARG* 3.9 4.9 - - + +
319C ASN* 3.2 16.9 + - - +
320C SER 3.1 0.4 - - - -
321C GLY* 1.3 77.8 - - - +
323C VAL* 1.3 57.4 + - - +
325C THR* 3.3 9.4 + - - -
326C ALA* 2.8 27.4 + - - +
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Residues in contact with VAL 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C VAL* 3.6 33.9 - - + -
308C ALA* 4.6 7.0 - - + -
312C ARG* 4.2 11.2 - - + -
317C PHE* 3.9 19.3 - - + -
319C ASN 4.0 9.2 - - - +
320C SER* 3.0 16.0 + - - +
322C ALA* 1.3 73.8 - - - +
324C ILE* 1.3 69.3 + - - +
326C ALA* 3.2 7.2 - - - +
327C MET* 3.1 24.5 + - + +
805C LMT 3.9 34.3 - - + -
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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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320C SER 3.6 6.7 + - - +
321C GLY* 3.2 13.0 + - - +
323C VAL* 1.3 76.9 - - - +
325C THR* 1.3 55.9 + - - +
327C MET* 2.8 47.6 + - + +
328C GLU* 2.9 20.1 + - + +
805C LMT 5.2 4.3 - - + -
20D HIS* 3.7 33.7 - - + +
22D THR* 3.9 16.4 - - + -
23D LEU* 4.0 42.8 - - + +
26D VAL* 4.2 11.9 - - + -
339D VAL* 4.4 3.1 - - + -
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Residues in contact with THR 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 GLY 3.0 15.1 + - - -
322C ALA* 3.6 12.1 - - - -
323C VAL 3.3 0.2 - - - -
324C ILE* 1.3 75.1 - - - +
326C ALA* 1.3 55.8 + - - +
328C GLU* 3.2 20.1 + - + +
329C VAL* 2.8 47.2 + - + +
20D HIS* 4.6 8.1 - - - -
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Residues in contact with ALA 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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95C VAL* 4.1 11.2 - - + -
98C GLN* 3.7 34.2 - - + +
317C PHE* 4.0 12.1 - - + -
322C ALA 2.8 14.3 + - - +
323C VAL* 3.2 15.7 - - - +
325C THR* 1.3 77.2 - - - +
327C MET* 1.3 52.9 + - - +
329C VAL* 3.5 3.5 + - - +
330C THR* 2.7 34.8 + - - -
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Residues in contact with MET 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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91C LEU* 4.0 35.2 - - + +
95C VAL* 3.6 19.5 - - + -
323C VAL 3.1 10.5 - - - +
324C ILE* 2.8 51.7 + - + +
326C ALA* 1.3 69.3 - - - +
328C GLU* 1.3 55.1 + - - +
330C THR* 3.0 10.2 + - - -
331C MET* 2.8 37.6 + - - +
805C LMT 4.6 16.8 - - + -
339D VAL* 3.9 12.8 - - + -
343D PHE* 3.6 32.5 - - + -
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Residues in contact with GLU 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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324C ILE* 2.9 20.0 + - + +
325C THR* 3.6 20.5 + - + +
327C MET* 1.3 76.0 - - - +
329C VAL* 1.3 61.4 + - + +
332C ALA* 3.0 20.1 + - - +
20D HIS* 3.2 34.7 + - - -
22D THR* 4.7 1.0 + - - -
335D ALA* 3.2 18.3 - - + +
336D GLY* 3.8 25.1 - - - +
339D VAL* 3.8 21.2 - - + +
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Residues in contact with VAL 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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98C GLN* 3.7 29.2 - - - +
325C THR* 2.8 37.6 + - + +
326C ALA 3.6 5.2 - - - +
328C GLU* 1.3 72.4 - - + +
330C THR* 1.3 62.4 + - - +
332C ALA* 3.4 8.1 + - - +
333C SER* 3.2 21.9 + - - -
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Residues in contact with THR 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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90C MET* 3.2 49.8 - - + +
94C GLY* 3.3 24.8 + - - -
98C GLN* 4.2 4.5 - - - +
326C ALA 2.7 19.4 + - - -
327C MET* 3.0 12.4 + - - -
329C VAL* 1.3 76.0 - - - +
331C MET* 1.3 65.0 + - + +
333C SER* 2.4 28.0 + - - +
334C MET* 3.1 10.9 - - - +
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Residues in contact with MET 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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87C LEU* 3.5 37.9 - - + +
90C MET* 3.9 19.5 - - + -
91C LEU* 3.5 27.8 - - + +
327C MET 2.8 20.7 + - - +
328C GLU 4.0 3.6 - - - +
330C THR* 1.3 74.5 - - + +
332C ALA* 1.3 61.9 + - - +
334C MET* 2.9 31.5 + - + +
335C ALA* 3.5 4.7 + - - -
338C LEU* 5.0 0.9 - - - +
77D PHE* 6.0 2.7 - - - -
331D MET 5.5 0.5 - - - +
332D ALA* 5.3 0.3 - - - -
335D ALA* 4.1 12.3 - - + -
338D LEU* 4.1 30.8 - - + +
339D VAL* 3.6 19.7 - - + -
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Residues in contact with ALA 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 GLU 3.0 16.8 + - - +
329C VAL* 3.7 8.3 - - - +
330C THR 3.3 0.2 - - - -
331C MET* 1.3 76.0 - - - +
333C SER* 1.3 60.2 + - - +
335C ALA* 3.3 20.8 - - - +
332D ALA* 3.5 37.5 - - + +
335D ALA* 3.7 3.9 - - + +
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Residues in contact with SER 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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90C MET* 5.6 1.4 - - - +
133C VAL* 6.1 0.9 - - - +
329C VAL* 3.2 11.6 + - - -
330C THR* 2.4 33.6 + - - +
332C ALA* 1.3 75.7 - - - +
334C MET* 1.3 61.2 + - - +
335C ALA* 3.2 5.7 + - - +
336C GLY* 4.4 4.2 + - - -
337C TYR 5.3 0.5 + - - -
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Residues in contact with MET 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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86C VAL* 3.8 18.4 - - + -
87C LEU* 3.7 28.9 - - + -
90C MET* 3.7 29.8 - - + +
330C THR 3.1 17.0 - - - +
331C MET* 2.9 26.8 + - + +
333C SER* 1.3 78.0 - - - +
335C ALA* 1.3 56.5 + - - +
336C GLY 3.3 2.5 - - - -
337C TYR* 3.3 33.1 + - + +
338C LEU* 2.9 32.0 + - + +
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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