Contacts of the helix formed by residues 16 - 27 (chain B) in PDB entry 3HCE
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 16 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14B PRO 4.0 2.8 + - - -
15B ASP* 1.3 76.5 + - - +
17B ALA* 1.3 75.9 + - - +
18B PRO 3.0 2.1 - - - -
19B GLY* 3.1 12.3 + - - -
20B GLN* 3.4 34.8 + - - +
196B ARG* 3.8 25.4 - - - +
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Residues in contact with ALA 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 3.3 12.7 + - - +
16B SER* 1.3 81.7 + - - +
18B PRO* 1.4 74.4 - - + +
20B GLN* 3.2 10.8 + - - +
21B ALA* 2.8 26.7 + - + +
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Residues in contact with PRO 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP* 3.4 30.3 - - + +
16B SER 3.3 5.6 - - - +
17B ALA* 1.4 94.2 - - + +
19B GLY* 1.3 62.5 + - - +
21B ALA* 3.3 7.9 + - + +
22B ALA* 3.1 21.7 + - - +
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Residues in contact with GLY 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASP 5.1 0.8 + - - -
16B SER 3.1 7.0 + - - -
18B PRO* 1.3 76.8 - - - +
20B GLN* 1.3 53.6 + - - +
22B ALA* 2.7 30.5 + - - +
23B VAL* 3.0 12.3 + - - +
189B PRO* 3.9 23.6 - - - +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B SER* 3.4 39.0 + - - +
17B ALA* 3.4 10.4 - - - +
19B GLY* 1.3 71.7 - - - +
21B ALA* 1.3 53.5 + - - +
22B ALA 3.2 0.3 + - - -
23B VAL* 3.3 8.9 + - - +
24B ALA* 2.8 35.9 + - - +
160B HIS* 3.5 55.9 + - + +
161B GLN* 4.4 9.5 + - - -
189B PRO* 4.0 4.9 - - + +
193B SER* 5.0 5.8 + - - +
196B ARG* 4.9 7.6 - - - +
200B HIS* 6.1 0.2 - - - -
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ALA 2.8 21.7 + - - +
18B PRO* 3.5 7.9 - - + +
20B GLN* 1.3 73.5 - - - +
22B ALA* 1.3 58.0 + - - +
24B ALA* 4.0 6.0 - - - +
25B SER* 3.0 27.7 + - - -
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B PRO 3.1 10.9 + - - +
19B GLY* 2.7 20.9 + - - +
21B ALA* 1.3 68.6 - - - +
23B VAL* 1.3 59.7 + - + +
25B SER* 3.2 7.6 + - - -
26B ALA* 2.9 28.2 + - - +
189B PRO* 6.4 0.2 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B GLY 3.0 10.8 + - - +
20B GLN* 3.4 9.4 - - - +
22B ALA* 1.3 71.2 - - + +
24B ALA* 1.3 72.1 + - - +
25B SER 2.9 1.4 + - - -
26B ALA* 2.9 16.4 + - - -
27B TYR* 3.2 34.4 + - + -
160B HIS* 4.5 6.5 - - + -
186B ALA 5.3 1.8 - - - +
187B VAL* 3.4 39.0 - - + +
189B PRO* 4.1 18.8 - - + -
230B THR 5.6 4.9 - - - +
290B SAH 4.6 6.1 - - - +
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN 2.8 20.2 + - - +
21B ALA* 4.0 8.3 - - - +
23B VAL* 1.3 76.9 - - - +
25B SER* 1.3 60.5 + - - +
27B TYR* 3.4 9.8 + - - +
28B GLN* 3.5 22.5 + - - +
102B PHE* 4.1 28.7 - - + -
290B SAH 6.3 0.4 - - - +
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Residues in contact with SER 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ALA 3.0 20.4 + - - -
22B ALA* 3.4 8.5 - - - -
23B VAL 2.9 1.4 + - - -
24B ALA* 1.3 76.6 - - - +
26B ALA* 1.3 61.7 + - - -
27B TYR 3.2 0.7 + - - -
28B GLN* 3.2 22.4 + - - +
29B ARG* 4.6 2.6 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA 2.9 12.0 + - - +
23B VAL* 2.9 14.1 + - - +
25B SER* 1.3 74.8 - - - +
27B TYR* 1.3 61.0 + - + +
28B GLN 3.2 0.7 + - - -
29B ARG* 3.4 17.2 + - - +
30B PHE 4.2 2.1 + - - -
228B ARG 6.0 0.7 - - - +
229B LEU* 4.6 29.0 - - + +
230B THR 5.7 2.2 - - - +
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Residues in contact with TYR 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.2 31.1 + - + -
24B ALA* 4.0 9.9 - - - +
25B SER 3.1 1.2 - - - -
26B ALA* 1.3 74.7 - - + +
28B GLN* 1.3 61.4 + - - +
29B ARG 2.9 7.3 + - - -
30B PHE* 3.3 34.5 + + + +
102B PHE* 5.0 2.9 - - + -
103B LEU* 3.4 31.9 - - + +
186B ALA* 2.6 38.5 + - - +
187B VAL* 3.5 18.2 - - + +
222B TYR* 2.7 30.7 + - - -
229B LEU* 3.8 22.0 - - + +
290B SAH 3.9 30.9 - + + +
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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