Contacts of the helix formed by residues 16 - 29 (chain B) in PDB entry 3H3B
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 5.9 0.9 - - - -
14B PRO* 4.0 3.7 - - - +
15B ALA* 1.3 82.9 - - - +
17B PRO* 1.3 70.0 - - - +
18B GLU* 3.5 20.3 + - - +
19B THR* 3.0 21.6 + - - +
20B HIS* 3.0 28.4 + - - +
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Residues in contact with PRO 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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15A ALA 5.0 13.2 - - - +
16A SER* 6.2 0.4 - - - -
17A PRO* 6.0 3.6 - - + -
14B PRO* 4.8 5.3 - - + +
15B ALA 4.6 1.3 - - - +
16B SER* 1.3 87.6 - - - +
18B GLU* 1.3 64.3 + - + +
20B HIS* 3.6 9.8 - - + +
21B LEU* 3.0 31.4 + - - +
42B TYR 5.2 5.4 - - - +
44B PRO* 5.0 22.5 - - + +
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Residues in contact with GLU 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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16B SER* 3.2 10.7 + - - +
17B PRO* 1.3 85.9 - - + +
19B THR* 1.3 63.9 + - + +
21B LEU* 4.2 4.6 - - - +
22B ASP* 3.3 22.2 + - - +
25B ARG* 4.8 2.1 + - - -
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Residues in contact with THR 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 ALA* 5.4 1.7 - - - +
16B SER* 3.0 32.4 + - - +
18B GLU* 1.3 78.3 - - + +
20B HIS* 1.3 58.2 + - - +
22B ASP* 3.5 7.9 + - - +
23B MET* 3.0 30.7 + - - +
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Residues in contact with HIS 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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9B MET* 3.6 35.2 - - + +
14B PRO* 3.6 32.6 - - + +
16B SER 3.0 19.0 + - - +
17B PRO* 3.6 8.5 - - + +
18B GLU 3.3 0.2 - - - -
19B THR* 1.3 74.8 + - - +
21B LEU* 1.3 66.2 + - - +
23B MET* 3.3 14.7 + - + +
24B LEU* 3.2 48.4 + - + +
39B GLU 5.9 0.2 - - - -
41B THR* 2.9 30.8 + - - -
42B TYR 4.8 4.3 - - - -
43B LEU* 4.4 7.2 - - + -
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Residues in contact with LEU 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 PRO 3.0 17.9 + - - +
18B GLU* 4.2 4.0 - - - +
20B HIS* 1.3 76.6 - - - +
22B ASP* 1.3 57.0 + - - +
24B LEU* 3.7 7.0 + - - +
25B ARG* 3.0 49.6 + - - +
43B LEU* 3.8 25.6 - - + -
44B PRO* 5.4 7.9 - - + -
47B ALA* 3.9 29.4 - - + -
48B SER* 3.9 19.3 - - - +
49B LEU* 4.4 1.1 - - + -
51B PHE* 4.3 9.6 - - + -
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Residues in contact with ASP 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 GLU 3.3 18.1 + - - +
19B THR* 3.6 9.6 - - - +
20B HIS 3.2 0.4 - - - -
21B LEU* 1.3 77.1 - - - +
23B MET* 1.3 60.8 + - - +
25B ARG* 3.3 30.2 + - - +
26B HIS* 2.9 37.7 + - - +
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Residues in contact with MET 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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7B THR* 4.7 9.9 - - - -
9B MET* 3.5 31.2 - - + -
19B THR 3.0 17.3 + - - +
20B HIS* 3.3 19.9 + - - +
22B ASP* 1.3 76.1 + - - +
24B LEU* 1.3 77.7 + - + +
26B HIS* 3.5 5.8 + - - +
27B LEU* 3.1 29.2 + - + +
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Residues in contact with LEU 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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7B THR* 4.9 3.6 - - + -
9B MET* 4.3 10.3 - - + -
20B HIS* 3.2 37.8 + - + +
21B LEU* 4.1 2.5 - - - +
23B MET* 1.3 95.4 - - + +
25B ARG* 1.3 58.7 + - - +
27B LEU* 4.5 1.6 - - - -
28B TYR* 2.9 49.8 + - + -
39B GLU 3.7 24.9 - - - +
40B LEU* 4.8 9.6 - - + -
43B LEU* 4.0 22.9 - - + -
51B PHE* 3.4 19.4 - - + -
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Residues in contact with ARG 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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18B GLU 4.8 2.2 + - - -
21B LEU* 3.0 38.8 + - - +
22B ASP* 3.3 47.8 + - - +
24B LEU* 1.3 75.8 - - - +
26B HIS* 1.3 62.3 + - - +
29B GLN* 2.9 38.1 + - + +
48B SER* 5.2 4.7 + - - -
51B PHE* 3.8 32.6 - - + -
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Residues in contact with HIS 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 ASP* 2.9 27.1 + - - +
23B MET* 3.9 5.8 - - - +
24B LEU 3.4 0.2 - - - -
25B ARG* 1.3 76.0 - - - +
27B LEU* 1.3 62.1 - - - +
29B GLN* 4.2 9.0 + - - +
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Residues in contact with LEU 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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4B CYS* 3.8 16.5 - - + +
5B THR* 3.5 44.9 - - + +
6B GLY 4.3 2.2 - - - +
7B THR* 3.9 19.7 - - + -
23B MET* 3.1 24.8 + - + +
24B LEU* 3.8 2.7 - - - +
26B HIS* 1.3 80.5 + - - +
28B TYR* 1.3 95.8 + - + +
29B GLN 3.7 3.1 + - - +
31B CYS* 4.3 1.0 - - - +
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Residues in contact with TYR 28 (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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4B CYS* 3.6 14.6 - - - -
5B THR 3.6 17.9 - - - -
6B GLY* 3.6 8.0 - - - -
7B THR* 3.7 6.8 + - - +
24B LEU* 2.9 47.5 + - + +
27B LEU* 1.3 87.3 - - + +
29B GLN* 1.3 63.1 + - - +
31B CYS* 3.1 19.8 + - - +
34B VAL* 3.9 22.4 - - + -
37B ASN 3.0 24.3 + - - -
38B LEU* 3.7 24.7 - - + -
39B GLU 4.1 4.0 + - - -
40B LEU* 5.2 1.3 - - + -
51B PHE* 2.9 33.3 - + + +
52B LEU* 4.6 0.9 - - + -
55B ILE* 4.2 17.0 - - + +
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Residues in contact with GLN 29 (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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2B GLN* 5.6 0.9 - - - +
25B ARG* 2.9 25.6 + - + +
26B HIS* 4.4 7.9 - - - +
27B LEU 3.4 4.5 - - - +
28B TYR* 1.3 73.9 - - - +
30B GLY* 1.3 71.8 + - - +
31B CYS* 3.2 3.5 + - - +
51B PHE* 3.9 25.0 + - + +
53B GLN* 5.8 4.8 + - - +
54B ASP* 5.3 2.2 + - - -
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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