Contacts of the helix formed by residues 12 - 27 (chain B) in PDB entry 3W1Y
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 12 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10B THR 4.3 0.4 + - - -
11B ARG* 1.3 75.7 - - - +
13B PHE* 1.3 65.8 + - - +
14B ALA* 3.5 8.8 + - - +
15B GLU* 3.1 31.2 + - - +
16B ARG* 3.1 18.3 + - - +
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Residues in contact with PHE 13 (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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12B SER* 1.3 71.6 - - - +
14B ALA* 1.3 62.4 + - + +
16B ARG* 3.2 28.5 + - - +
17B ALA* 2.9 39.5 + - + -
118B ASP* 4.4 2.7 - - - -
119B PRO* 3.5 35.9 - - + -
120B ASP* 3.5 27.6 - - + -
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 3.1 7.9 + - - +
13B PHE* 1.3 84.1 - - + +
15B GLU* 1.3 57.2 + - - +
17B ALA* 3.5 5.9 + - - +
18B LYS* 3.1 42.7 + - - +
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Residues in contact with GLU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ARG* 2.5 42.7 + - - +
12B SER* 3.1 25.4 + - - +
14B ALA* 1.3 75.0 - - + +
16B ARG* 1.3 58.2 + - - +
18B LYS* 3.3 25.0 + - - +
19B GLU* 3.0 31.9 + - - +
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B TYR* 3.8 27.4 - - + -
8B GLN* 3.0 42.8 + - - +
11B ARG* 2.9 32.7 + - + -
12B SER 3.1 5.9 + - - +
13B PHE* 3.4 37.1 - - - +
15B GLU* 1.3 74.5 - - - +
17B ALA* 1.3 65.3 + - - +
19B GLU* 3.2 17.9 + - - +
20B THR* 3.2 18.5 + - - +
118B ASP* 4.4 2.8 + - - -
120B ASP* 2.8 54.7 + - + +
122B PHE* 4.0 2.6 - - + -
124B TYR* 3.4 10.5 - - - -
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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
----------------------------------------------------------
13B PHE* 2.9 36.3 + - + +
14B ALA* 3.6 7.2 - - - +
16B ARG* 1.3 73.6 - - - +
18B LYS* 1.3 62.0 + - - +
20B THR* 3.2 1.0 + - - -
21B GLU* 2.7 48.3 + - - +
119B PRO 5.6 0.4 - - - +
120B ASP* 3.6 16.0 + - - +
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Residues in contact with LYS 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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14B ALA* 3.1 35.0 + - - +
15B GLU* 3.3 28.1 - - - +
16B ARG 3.2 0.2 - - - -
17B ALA* 1.3 76.9 - - - +
19B GLU* 1.3 62.3 + - + +
21B GLU* 4.0 5.4 - - - +
22B SER* 3.1 26.7 + - - -
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Residues in contact with GLU 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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7B TYR* 2.8 26.9 + - - -
11B ARG* 2.3 36.7 + - - +
15B GLU 3.0 15.9 + - - +
16B ARG* 3.2 7.8 + - - +
18B LYS* 1.3 76.3 - - + +
20B THR* 1.3 57.9 + - - +
22B SER* 3.5 4.8 + - - -
23B ALA* 2.9 29.4 + - - +
66B LYS* 3.2 15.7 + - + -
122B PHE* 3.4 25.8 - - + -
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Residues in contact with THR 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 ARG 3.2 1.8 + - - +
17B ALA 3.2 5.9 + - - -
19B GLU* 1.3 74.0 - - - +
21B GLU* 1.3 73.6 + - - +
23B ALA* 3.4 5.5 + - - +
24B ARG* 2.9 35.0 + - - +
32B PRO* 4.1 10.8 - - + -
120B ASP 2.6 25.9 + - - +
121B GLY* 3.7 10.1 - - - -
122B PHE* 3.3 53.8 - - + +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 2.7 48.2 + - - +
18B LYS* 4.0 5.2 - - - +
20B THR* 1.3 89.2 + - - +
22B SER* 1.3 56.4 + - - +
24B ARG* 3.3 5.2 + - - +
25B LEU* 3.1 37.2 + - + +
119B PRO 5.6 0.5 - - - +
120B ASP 4.1 3.6 - - - +
121B GLY* 5.3 1.6 - - - -
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Residues in contact with SER 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 LYS 3.1 18.8 + - - -
19B GLU* 3.7 4.9 - - - -
21B GLU* 1.3 75.3 - - - +
23B ALA* 1.3 64.3 + - - +
25B LEU* 3.4 3.3 + - - -
26B ARG* 2.6 56.6 + - - +
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Residues in contact with ALA 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 GLU 2.9 19.8 + - - +
20B THR* 3.9 6.3 - - - +
22B SER* 1.3 73.1 + - - +
24B ARG* 1.3 59.9 + - + +
26B ARG* 3.6 5.1 + - - +
27B TYR* 2.8 35.6 + - - +
32B PRO* 5.0 4.7 - - + -
68B LEU* 3.8 31.3 - - + +
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 2.9 24.5 + - - +
21B GLU* 4.0 4.9 - - - +
23B ALA* 1.3 75.7 - - + +
25B LEU* 1.3 65.1 + - - +
27B TYR 3.9 5.8 - - - -
28B PRO* 3.2 45.3 + - - +
29B LYS 5.9 0.2 - - - -
30B HIS 3.8 18.8 + - - +
31B ILE* 4.8 4.6 - - - +
32B PRO* 3.9 15.4 - - + +
68B LEU* 6.0 0.2 - - + -
71B GLU* 5.3 5.5 + - - +
113B TYR* 3.4 42.9 + - - -
121B GLY* 5.1 0.4 - - - -
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Residues in contact with LEU 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 GLU* 3.1 22.7 + - + +
22B SER* 3.8 1.3 - - - +
23B ALA 3.4 0.2 - - - -
24B ARG* 1.3 79.2 - - - +
26B ARG* 1.3 84.8 + - - +
27B TYR 3.4 0.7 + - - -
28B PRO* 3.6 9.2 - - - +
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Residues in contact with ARG 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B SER* 2.6 55.9 + - - +
23B ALA* 4.1 2.2 - - - +
25B LEU* 1.3 105.8 - - - +
27B TYR* 1.3 87.6 + - + +
28B PRO* 3.7 4.8 - - - +
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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 ALA* 2.8 17.4 + - - +
24B ARG* 3.6 5.0 - - - +
26B ARG* 1.3 98.8 - - + +
28B PRO* 1.3 62.4 - - - +
29B LYS 3.1 3.4 - - - -
30B HIS* 2.9 61.4 + + + +
68B LEU* 3.6 29.6 - - + -
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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