Contacts of the helix formed by residues 17 - 25 (chain C) in PDB entry 3ELP
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 HIS 17 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C PHE 3.6 0.6 + - - -
16C GLN* 1.3 98.1 + - + +
18C PHE* 1.3 61.9 + - - +
20C THR* 3.0 4.5 + - + -
21C GLN* 2.8 50.0 + - + +
382D ASP* 2.7 22.2 + - - +
384D GLU* 3.9 7.9 + - - -
385D ASP* 2.9 39.8 + - - +
388D GLU* 5.6 1.6 + - - -
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Residues in contact with PHE 18 (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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15C PHE* 3.6 23.1 + + + +
16C GLN 3.0 6.6 + - - -
17C HIS* 1.3 74.6 - - - +
19C ALA* 1.3 63.1 + - - +
21C GLN* 3.1 8.6 + - - -
22C ALA* 2.8 35.1 + - + +
78C LEU* 3.4 64.0 - - + +
193C PRO* 3.7 17.7 - - + -
194C TYR* 3.7 42.8 - + + -
197C ARG* 4.3 9.4 - - - +
262C LEU* 3.9 18.2 - - + -
263C HIS* 4.4 8.7 - - + -
382D ASP* 2.9 3.3 + - - +
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Residues in contact with ALA 19 (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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18C PHE* 1.3 80.1 - - - +
20C THR* 1.3 63.4 + - - +
22C ALA* 3.3 5.3 + - - +
23C ILE* 3.0 29.6 + - - +
263C HIS* 3.1 42.4 - - + +
268D LYS* 5.6 0.9 - - - +
380D LEU 3.5 8.5 - - - +
381D GLU* 3.9 2.7 - - - -
382D ASP* 3.0 24.0 + - - +
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Residues in contact with THR 20 (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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17C HIS* 3.0 6.6 + - + -
19C ALA* 1.3 77.6 - - - +
21C GLN* 1.3 55.2 + - + +
23C ILE 3.4 0.2 + - - -
24C HIS* 2.8 46.5 + - + +
334D LEU* 3.5 33.0 - - + -
381D GLU* 3.4 12.4 - - + +
382D ASP* 3.0 21.2 + - - +
385D ASP* 3.0 28.7 + - + +
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Residues in contact with GLN 21 (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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16C GLN 4.3 4.2 + - - +
17C HIS* 2.8 54.5 + - + +
18C PHE* 3.6 12.5 + - - +
20C THR* 1.3 70.3 - - + +
22C ALA* 1.3 64.4 + - - +
24C HIS* 5.1 0.2 - - - -
25C VAL* 2.8 53.4 + - + +
74C ALA* 5.0 2.8 - - - +
77C ALA* 3.4 36.7 + - + +
78C LEU* 4.1 7.8 + - + +
197C ARG* 5.0 2.8 + - - -
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Residues in contact with ALA 22 (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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18C PHE* 2.8 21.3 + - + +
19C ALA* 3.6 9.0 - - - +
21C GLN* 1.3 79.3 - - - +
23C ILE* 1.3 58.7 + - + +
25C VAL 5.2 0.5 - - - +
27C GLN* 4.7 2.9 + - - -
74C ALA* 5.4 6.5 - - - +
78C LEU* 3.8 22.4 - - + +
256C ASN* 4.7 4.5 - - - +
259C LEU* 3.6 27.6 - - + +
260C LYS* 3.6 23.5 + - - +
263C HIS* 6.2 2.0 - - + -
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Residues in contact with ILE 23 (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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19C ALA* 3.0 14.9 + - - +
20C THR 4.0 2.2 - - - +
22C ALA* 1.3 79.4 - - + +
24C HIS* 1.3 68.5 + - + +
27C GLN* 3.0 21.2 - - - +
260C LYS* 3.6 35.5 + - + +
263C HIS* 4.9 0.7 - - - +
344D PHE* 3.3 34.3 - - + +
345D GLU* 3.6 31.9 - - + +
380D LEU* 3.6 34.8 - - + +
381D GLU* 3.9 2.7 - - - +
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Residues in contact with HIS 24 (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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20C THR* 2.8 29.6 + - + +
21C GLN* 5.1 0.2 - - - -
23C ILE* 1.3 80.8 + - + +
25C VAL* 1.3 62.7 + - + +
26C GLY 3.1 4.3 + - - -
27C GLN* 3.3 18.0 + - - +
334D LEU* 3.7 34.7 - - + +
336D THR* 4.9 5.4 - - - -
345D GLU* 3.8 30.7 + - + -
346D SER 5.1 0.2 - - - -
381D GLU* 2.9 43.4 + - + +
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Residues in contact with VAL 25 (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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21C GLN* 2.8 51.6 + - + +
22C ALA 5.2 0.3 - - - +
23C ILE 3.9 0.4 - - - -
24C HIS* 1.3 69.0 - - + +
26C GLY* 1.3 60.4 + - - +
27C GLN* 3.2 16.0 + - - -
70C CYS 4.2 0.7 - - - +
73C LYS* 3.8 19.1 - - + +
74C ALA* 3.7 38.8 - - - +
77C ALA* 4.4 8.5 - - + -
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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