Contacts of the helix formed by residues 18 - 31 (chain B) in PDB entry 1YWT
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 ARG 18 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A GLY 5.1 2.8 + - - +
55A GLN* 4.2 24.2 - - - +
58A ALA* 3.4 23.1 - - + -
84A TYR* 3.4 17.8 + - - +
87A LYS* 4.7 0.2 - - - +
88A VAL* 3.9 18.7 - - - +
91A GLU* 3.0 35.5 + - - -
13B ALA* 2.9 13.1 + - - +
16B ALA* 3.7 13.9 - - - +
17B GLU* 1.3 74.3 - - - +
19B TYR* 1.3 59.1 + - - +
20B GLU* 3.3 3.1 - - - -
21B ASP* 2.9 39.4 + - + +
22B MET* 2.9 25.2 + - - +
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Residues in contact with TYR 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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14B GLU* 4.5 12.4 + - + +
17B GLU* 3.6 47.2 + - + +
18B ARG* 1.3 68.2 - - - +
20B GLU* 1.3 62.1 + - - +
22B MET* 3.5 23.0 - - - +
23B ALA* 2.8 32.1 + - - +
46B VAL* 4.4 9.4 - - + -
47B ALA* 4.1 6.5 - - - +
50B ASN* 3.3 54.8 + - + -
51B VAL* 3.6 9.3 - - + +
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Residues in contact with GLU 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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20A GLU* 5.1 6.1 - - - +
18B ARG 3.3 1.0 - - - -
19B TYR* 1.3 77.8 - - - +
21B ASP* 1.3 67.5 + - - +
23B ALA* 3.4 3.2 + - - +
24B ALA* 3.2 21.1 + - - +
51B VAL* 3.9 22.3 - - + +
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Residues in contact with ASP 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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84A TYR* 3.0 33.6 + - + +
87A LYS* 3.3 23.6 + - - -
88A VAL* 4.8 0.3 - - - +
91A GLU* 4.7 1.0 - - - +
18B ARG* 2.9 43.8 + - - +
20B GLU* 1.3 83.2 - - - +
22B MET* 1.3 63.0 + - - +
24B ALA* 3.2 8.5 + - - +
25B PHE* 3.0 33.8 + - + -
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Residues in contact with MET 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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10B ALA* 3.7 16.3 - - + +
13B ALA* 3.4 19.2 - - + +
14B GLU* 3.4 37.7 - - + +
18B ARG 2.9 9.8 + - - +
19B TYR* 3.2 20.2 + - - +
21B ASP* 1.3 77.9 - - - +
23B ALA* 1.3 61.8 + - - +
25B PHE* 3.4 6.0 + - - +
26B MET* 3.1 23.9 + - + +
43B LEU* 3.3 52.9 - - + +
46B VAL* 4.3 3.1 - - + -
47B ALA* 3.5 21.3 - - + +
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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 TYR 2.8 20.1 + - - +
20B GLU* 3.8 4.5 - - + +
22B MET* 1.3 72.5 - - - +
24B ALA* 1.3 59.0 + - - +
26B MET* 3.6 3.6 + - - +
27B LYS* 3.0 27.5 + - - +
47B ALA* 3.4 19.2 - - + +
48B TYR* 3.6 38.9 + - + -
51B VAL* 4.1 9.4 - - + -
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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 GLU 3.2 9.8 + - - +
21B ASP* 3.2 12.2 + - - +
23B ALA* 1.3 76.5 - - - +
25B PHE* 1.3 68.1 + - + +
27B LYS* 3.1 10.7 + - - +
28B GLY* 3.0 18.5 + - - -
48B TYR* 5.1 1.1 - - - -
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Residues in contact with PHE 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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84A TYR* 3.6 38.4 - + - -
87A LYS* 5.5 7.9 - - + -
1B MET* 4.8 8.5 - - + -
6B LEU* 3.6 38.6 - - + +
9B LYS* 3.5 56.5 - - + -
10B ALA* 3.8 5.4 - - + -
13B ALA* 4.4 0.2 - - + -
21B ASP* 3.0 30.7 + - + -
22B MET* 3.4 5.8 + - - +
24B ALA* 1.3 78.3 - - + +
26B MET* 1.3 64.3 + - - +
28B GLY* 2.8 13.7 + - - -
29B ALA* 2.9 12.7 + - - +
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Residues in contact with MET 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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7B ILE* 3.8 32.1 - - + -
10B ALA* 3.9 17.3 - - + -
22B MET* 3.1 18.9 + - + +
23B ALA* 3.8 6.1 - - - +
25B PHE* 1.3 79.3 - - - +
27B LYS* 1.3 58.2 + - - +
29B ALA* 3.1 6.9 + - + +
30B VAL* 2.9 35.6 + - - +
36B LEU* 4.3 18.2 - - + -
40B GLU* 3.7 21.1 - - + +
43B LEU* 3.8 20.9 - - + +
44B LEU* 3.8 31.6 - - + +
47B ALA* 4.9 0.7 - - + -
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Residues in contact with LYS 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 3.0 14.4 + - - +
24B ALA* 3.1 12.1 + - - +
26B MET* 1.3 75.9 - - - +
28B GLY* 1.3 61.4 + - - +
30B VAL* 3.3 1.8 + - - +
31B GLU* 2.9 60.4 + - - +
44B LEU* 4.9 0.2 - - - +
48B TYR* 3.8 14.8 - - - +
98B THR* 4.4 16.4 - - + +
102B LEU* 3.9 30.7 - - + -
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Residues in contact with GLY 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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6B LEU* 3.6 16.2 - - - +
24B ALA 3.0 8.3 + - - -
25B PHE 2.8 8.6 + - - -
27B LYS* 1.3 77.8 - - - +
29B ALA* 1.3 61.7 + - - +
30B VAL 3.5 0.2 + - - -
31B GLU* 3.6 11.5 + - - +
32B LYS* 3.2 24.4 + - - +
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Residues in contact with ALA 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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3B ARG* 3.8 18.9 + - + +
6B LEU* 3.7 15.3 - - + +
7B ILE* 4.0 29.6 - - + +
25B PHE 2.9 11.2 + - - +
26B MET* 3.1 14.1 + - + +
28B GLY* 1.3 74.9 - - - +
30B VAL* 1.3 63.9 + - - +
32B LYS* 3.1 25.8 - - - +
33B GLY 4.5 0.2 + - - -
34B GLU 4.6 1.6 - - - +
36B LEU* 5.1 2.0 - - + -
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Residues in contact with VAL 30 (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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26B MET* 2.9 23.6 + - + +
27B LYS* 3.6 8.1 - - - +
29B ALA* 1.3 72.0 - - - +
31B GLU* 1.3 59.0 + - - +
32B LYS 2.9 10.4 + - - -
33B GLY* 3.1 14.0 + - - -
34B GLU 4.4 2.3 - - - +
36B LEU* 4.0 32.5 - - + -
44B LEU* 4.4 14.6 - - + -
102B LEU* 3.8 22.2 - - + -
106B HIS* 3.7 32.5 + - + +
107B LEU* 4.0 13.0 - - + -
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Residues in contact with GLU 31 (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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27B LYS* 2.9 53.2 + - - +
28B GLY* 3.6 9.5 + - - +
29B ALA 3.4 0.2 - - - -
30B VAL* 1.3 71.0 - - - +
32B LYS* 1.3 59.9 + - - +
33B GLY* 3.0 7.8 + - - -
102B LEU* 4.1 13.1 - - + +
106B HIS* 3.9 14.4 - - + +
249B CA 3.4 22.1 - - - -
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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