Contacts of the helix formed by residues 325 - 336 (chain C) in PDB entry 4HRE
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 GLY 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324C LYS* 1.3 73.4 - - - +
326C ASP* 1.3 62.2 + - - -
327C TYR 3.1 2.7 - - - -
328C GLN* 2.9 20.7 + - - +
329C LYS* 3.0 23.1 + - - +
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Residues in contact with ASP 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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53C GLU* 2.8 35.0 - - - +
54C VAL* 3.6 28.2 - - - +
57C VAL* 4.3 11.7 - - + +
95C LEU* 4.0 12.4 - - + +
325C GLY* 1.3 69.0 - - - -
327C TYR* 1.3 56.8 + - - +
329C LYS* 3.6 13.6 - - + +
330C ALA* 2.7 36.2 + - - +
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Residues in contact with TYR 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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94C HIS* 3.4 43.3 - + + -
95C LEU* 4.0 22.9 - - + +
98C VAL* 3.5 25.6 - - + -
285C ASP* 2.9 30.8 + - - +
288C LEU* 4.1 4.0 - - - +
289C ILE* 3.4 21.9 - - + +
323C THR* 3.6 23.6 - - + -
324C LYS 4.2 11.2 - - - +
325C GLY 3.1 0.2 - - - -
326C ASP* 1.3 78.2 - - - +
328C GLN* 1.3 62.3 + - - +
330C ALA* 3.2 2.9 + - - +
331C LEU* 3.1 42.2 + - + +
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Residues in contact with GLN 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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320C GLN* 3.3 27.7 + - - +
323C THR* 2.6 53.4 + - - +
324C LYS* 3.7 10.7 + - - +
325C GLY 2.9 10.4 + - - +
327C TYR* 1.3 80.9 - - - +
329C LYS* 1.3 81.7 + - - +
331C LEU* 3.1 5.1 + - - +
332C LEU* 2.8 56.0 + - + +
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Residues in contact with LYS 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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57C VAL* 5.3 2.0 - - + -
325C GLY 3.0 18.8 + - - +
326C ASP* 3.2 17.9 + - + +
328C GLN* 1.3 97.4 + - - +
330C ALA* 1.3 57.9 + - - +
332C LEU* 3.7 11.3 - - + +
333C TYR* 2.9 51.7 + - + +
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Residues in contact with ALA 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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57C VAL* 4.0 20.2 - - + +
61C THR* 4.2 10.3 - - + +
95C LEU* 4.0 14.1 - - + -
98C VAL* 4.5 13.7 - - + -
99C ILE* 5.3 0.4 - - + -
326C ASP 2.7 17.5 + - - +
327C TYR 3.3 6.1 - - - +
329C LYS* 1.3 74.2 - - - +
331C LEU* 1.3 65.1 + - - +
333C TYR* 3.7 5.0 - - - +
334C LEU* 2.9 30.0 + - - +
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Residues in contact with LEU 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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98C VAL* 4.4 15.7 - - + -
288C LEU* 3.8 14.8 - - + -
289C ILE* 4.7 7.9 - - + -
292C MET* 3.5 26.4 - - + +
319C ILE* 3.5 22.4 - - + -
323C THR* 3.6 33.4 - - + +
327C TYR* 3.1 37.9 + - + +
328C GLN 3.1 5.6 + - - +
330C ALA* 1.3 76.8 - - - +
332C LEU* 1.3 52.0 + - - +
334C LEU* 3.1 7.0 + - + +
335C CYS* 2.6 34.5 + - - +
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Residues in contact with LEU 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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316C TYR* 3.5 62.2 - - + +
319C ILE* 3.6 20.6 - - + -
320C GLN* 3.8 12.8 - - + +
328C GLN* 2.8 48.8 + - + +
329C LYS* 3.7 12.1 - - + +
331C LEU* 1.3 73.6 - - - +
333C TYR* 1.3 61.4 + - + +
335C CYS* 3.1 4.0 + - + +
336C GLY* 2.8 26.9 + - - -
337C GLY 4.3 2.8 + - - -
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Residues in contact with TYR 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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26C SER* 4.9 2.9 + - - +
27C VAL* 4.9 4.7 - - - +
57C VAL* 4.4 5.6 - - + -
58C ASN* 3.0 37.3 + - + +
61C THR* 3.0 40.0 - - - +
62C ASN* 4.2 15.5 - - - +
329C LYS* 2.9 38.3 + - + +
330C ALA* 3.7 4.3 - - - +
332C LEU* 1.3 74.9 - - + +
334C LEU* 1.3 65.7 + - - +
335C CYS 3.3 0.5 + - - -
336C GLY* 3.3 13.8 + - - -
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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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26C SER* 2.7 26.2 + - - -
27C VAL* 3.9 25.8 - - + +
61C THR* 4.6 9.9 - - - +
68C ARG* 4.4 4.0 - - - +
98C VAL* 4.0 23.6 - - + -
102C LEU* 3.7 39.3 - - + -
292C MET* 3.9 30.0 - - + +
293C VAL* 4.1 6.5 - - + -
296C SER* 4.2 8.2 - - - -
300C MET* 4.2 7.4 - - - +
330C ALA 2.9 15.5 + - - +
331C LEU* 3.3 12.1 - - + +
333C TYR* 1.3 77.4 - - - +
335C CYS* 1.3 52.9 + - - +
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Residues in contact with CYS 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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26C SER* 3.1 17.5 + - - -
292C MET* 3.6 14.6 - - + +
300C MET* 3.7 8.3 - - - +
304C ARG* 3.2 29.5 + - - -
315C LEU* 4.4 5.4 - - - -
316C TYR* 4.1 22.7 - - - -
319C ILE* 4.0 7.2 - - + -
331C LEU 2.6 15.9 + - - +
332C LEU* 3.1 12.8 + - + +
334C LEU* 1.3 74.0 - - - +
336C GLY* 1.3 58.0 + - - +
337C GLY 3.3 22.0 - - - -
339C ASP* 5.7 0.2 - - - -
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Residues in contact with GLY 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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26C SER* 4.2 11.7 - - - -
304C ARG* 3.8 10.8 + - - -
332C LEU 2.8 15.1 + - - -
333C TYR* 3.3 12.2 + - - -
335C CYS* 1.3 74.2 - - - +
337C GLY* 1.3 54.7 + - - +
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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