Contacts of the helix formed by residues 23 - 39 (chain B) in PDB entry 4YYH
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 THR 23 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A LYS* 4.2 14.1 - - - +
22B SER* 1.3 75.9 - - - +
24B PRO* 1.3 69.8 - - + +
25B ILE* 3.5 8.1 + - - +
26B GLN* 2.7 42.8 + - - +
27B GLN* 2.9 28.9 + - - +
77B ASN* 4.4 13.5 + - - +
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Residues in contact with PRO 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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22B SER 4.5 0.9 - - - +
23B THR* 1.3 89.7 - - - +
25B ILE* 1.3 61.0 + - + +
27B GLN* 3.3 18.6 + - - +
28B LEU* 3.1 22.3 + - - +
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Residues in contact with ILE 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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23B THR* 3.2 8.4 + - - +
24B PRO* 1.3 74.7 - - + +
26B GLN* 1.4 69.4 + - + +
28B LEU* 3.2 11.3 + - + +
29B LEU* 3.0 42.6 + - + +
79B TYR 4.3 13.0 - - - +
80B LYS 4.3 18.6 - - - +
81B SER* 5.1 4.7 - - - +
82B VAL* 5.5 1.6 - - + +
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Residues in contact with GLN 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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115A HIS* 5.0 2.2 - - - -
119A LYS* 4.3 2.6 + - - +
21B GLU 4.1 3.6 + - - +
22B SER* 3.1 21.4 - - - +
23B THR* 2.7 46.8 + - - +
25B ILE* 1.4 78.9 - - + +
27B GLN* 1.3 58.6 + - - +
29B LEU* 3.3 3.2 + - + -
30B GLU* 2.8 36.3 + - + +
74B ILE* 2.9 39.2 + - + +
75B VAL* 3.4 18.2 + - - +
77B ASN* 3.3 29.5 + - - +
79B TYR 6.1 0.2 - - - +
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Residues in contact with GLN 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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21B GLU* 5.2 1.9 - - - +
22B SER* 2.8 39.6 + - - +
23B THR 2.9 18.3 + - - +
24B PRO* 3.7 13.2 - - - +
25B ILE 3.2 0.4 - - - -
26B GLN* 1.3 76.8 - - - +
28B LEU* 1.3 63.1 + - - +
30B GLU* 3.4 7.9 + - - +
31B HIS* 3.0 23.4 + - - +
34B ARG* 4.8 1.6 + - - -
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Residues in contact with LEU 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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24B PRO 3.1 13.1 + - - +
25B ILE* 3.5 14.1 - - + +
27B GLN* 1.3 76.4 - - - +
29B LEU* 1.3 60.1 + - + +
31B HIS* 3.1 12.9 + - + +
32B PHE* 2.9 55.8 + - + +
82B VAL* 3.6 29.4 - - + -
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Residues in contact with LEU 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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25B ILE* 3.0 34.9 + - + +
26B GLN* 3.9 4.5 - - + +
28B LEU* 1.3 79.1 - - + +
30B GLU* 1.3 56.6 + - - +
32B PHE* 3.3 9.2 + - + +
33B LEU* 2.8 30.1 + - - +
74B ILE* 3.7 19.7 - - + +
79B TYR* 3.5 40.8 - - + +
81B SER 4.5 2.0 - - - +
82B VAL* 3.9 29.6 - - + +
85B PHE* 3.7 30.1 - - + -
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Residues in contact with GLU 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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22B SER* 6.0 2.9 - - - +
26B GLN* 2.8 24.3 + - + +
27B GLN* 3.7 6.5 - - - +
28B LEU 3.3 0.2 - - - -
29B LEU* 1.3 74.6 - - - +
31B HIS* 1.3 63.8 + - - +
33B LEU* 3.4 4.4 + - - +
34B ARG* 3.0 48.5 + - - +
71B LYS* 3.4 31.9 + - - +
74B ILE* 3.7 23.9 - - + +
75B VAL* 3.8 21.8 - - - +
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Residues in contact with HIS 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 GLN 3.0 14.2 + - - +
28B LEU* 3.5 14.8 - - + +
30B GLU* 1.3 78.5 - - - +
32B PHE* 1.3 81.2 + + - +
34B ARG* 3.4 22.5 + - - +
35B GLN* 3.1 47.4 + - + +
120B MET* 6.3 0.2 - - - -
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Residues in contact with PHE 32 (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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28B LEU* 2.9 44.7 + - + +
29B LEU* 3.6 19.5 - - + +
31B HIS* 1.3 88.9 - + - +
33B LEU* 1.3 59.5 + - - +
35B GLN* 3.2 2.4 + - - +
36B LEU* 2.9 34.5 + - - +
82B VAL* 4.0 21.5 - - + -
85B PHE* 3.8 12.8 - + + -
120B MET* 3.8 18.6 - - + -
121B MET* 3.7 51.6 - - + -
123B LYS* 5.5 4.5 - - - -
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Residues in contact with LEU 33 (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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29B LEU 2.8 21.4 + - - +
30B GLU* 3.7 6.3 - - - +
31B HIS 3.3 0.2 - - - -
32B PHE* 1.3 74.4 - - - +
34B ARG* 1.3 57.3 + - + +
36B LEU* 3.2 3.2 + - + +
37B GLN* 2.8 42.3 + - + +
67B PHE* 3.5 40.4 - - + +
70B MET* 4.4 6.5 - - + -
71B LYS* 3.6 47.8 - - + +
74B ILE* 3.9 11.4 - - + -
85B PHE* 3.9 17.9 - - + -
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Residues in contact with ARG 34 (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 GLN 4.8 1.6 + - - -
30B GLU* 3.0 38.0 + - - +
31B HIS* 3.6 33.5 + - - +
33B LEU* 1.3 76.7 - - + +
35B GLN* 1.4 65.2 + - - +
37B GLN* 3.4 7.8 + - - +
38B ARG* 3.1 45.2 + - - +
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Residues in contact with GLN 35 (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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31B HIS* 3.1 40.9 + - + +
32B PHE 3.6 5.2 - - - +
34B ARG* 1.4 77.1 + - - +
36B LEU* 1.3 63.8 + - - +
38B ARG* 3.1 52.9 + - - +
39B LYS* 3.7 13.4 + - - +
120B MET* 3.5 30.0 - - + -
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Residues in contact with LEU 36 (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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32B PHE 2.9 21.2 + - - +
33B LEU* 3.6 4.7 - - + +
35B GLN* 1.3 74.8 - - - +
37B GLN* 1.3 65.0 + - - +
39B LYS* 3.0 26.6 + - + +
40B ASP* 3.9 2.1 + - - +
67B PHE* 3.8 24.8 - - + -
70B MET* 5.1 0.4 - - + -
85B PHE* 3.8 31.0 - - + -
89B PHE* 3.9 34.5 - - + -
113B ILE* 5.0 1.6 - - - +
117B GLY* 3.6 31.9 - - - -
120B MET* 3.7 16.4 - - + -
121B MET* 4.3 6.1 - - + -
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Residues in contact with GLN 37 (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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33B LEU* 2.8 37.8 + - + +
34B ARG* 3.8 7.0 - - - +
36B LEU* 1.3 72.9 - - - +
38B ARG* 1.3 55.6 + - - +
40B ASP* 2.9 31.2 + - - +
41B PRO* 4.7 0.5 - - - +
43B GLY* 6.2 0.4 - - - -
46B ALA* 4.5 16.2 + - - +
67B PHE* 3.5 51.4 - - + +
71B LYS* 5.7 1.6 - - - +
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Residues in contact with ARG 38 (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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34B ARG* 3.1 36.2 + - - +
35B GLN* 3.1 43.7 + - - +
36B LEU 3.2 0.4 - - - -
37B GLN* 1.3 75.7 - - - +
39B LYS* 1.3 60.5 + - + +
40B ASP 3.2 1.5 + - - -
41B PRO* 3.7 15.2 - - - +
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Residues in contact with LYS 39 (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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35B GLN 3.7 12.7 + - - +
36B LEU* 3.0 19.4 + - + +
38B ARG* 1.3 78.1 - - + +
40B ASP* 1.3 55.2 + - - +
41B PRO* 3.3 10.3 - - - +
109B LEU* 3.6 19.6 - - - +
113B ILE* 3.7 25.2 - - + +
116B ALA* 4.4 34.5 + - + +
117B GLY* 4.6 5.2 - - - +
120B MET* 4.2 26.2 - - - +
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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