Contacts of the helix formed by residues 38 - 50 (chain B) in PDB entry 5HAN
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 ASN 38 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B PRO* 4.3 2.9 - - - -
37B GLY* 1.3 72.0 - - - -
39B PHE* 1.3 63.3 + - - +
40B ILE* 3.3 14.3 + - - +
41B GLN* 2.9 49.8 + - - +
42B THR* 2.8 26.2 + - - -
77B GLU* 5.9 0.9 - - - +
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Residues in contact with PHE 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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30B MET* 3.3 44.5 - - + +
32B PRO* 3.9 22.3 - - + +
38B ASN* 1.3 74.8 - - - +
40B ILE* 1.3 58.8 + - - +
42B THR 3.4 0.2 + - - -
43B ALA* 2.9 30.6 + - + +
75B VAL* 3.9 27.6 - - + -
77B GLU* 3.6 53.1 + - + +
80B SER* 3.8 22.0 - - - -
81B LEU 3.3 29.8 - - - -
82B MET* 4.4 2.5 - - + -
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Residues in contact with ILE 40 (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 SER* 3.9 15.3 - - - +
8B ALA* 3.9 27.1 - - + -
10B LEU* 4.1 21.1 - - + -
38B ASN* 3.3 16.3 + - - +
39B PHE* 1.3 77.5 - - - +
41B GLN* 1.3 66.4 + - + +
43B ALA* 3.7 2.0 - - + +
44B ALA* 2.9 30.8 + - - +
72B VAL* 4.1 9.0 - - + -
75B VAL* 4.0 28.5 - - + -
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Residues in contact with GLN 41 (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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1B MET 5.5 2.2 - - - +
2B ASP* 3.2 45.3 + - - +
3B GLN 5.2 3.3 + - - +
4B SER* 3.5 9.9 - - - +
37B GLY* 3.3 13.4 - - - -
38B ASN* 2.9 49.3 + - - +
40B ILE* 1.3 78.3 - - + +
42B THR* 1.4 56.6 + - - +
44B ALA* 3.5 2.9 + - - +
45B HIS* 3.1 27.4 + - - +
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Residues in contact with THR 42 (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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30B MET* 3.9 17.5 - - - -
32B PRO* 3.6 12.8 - - + +
37B GLY* 3.3 19.8 + - - -
38B ASN 2.8 22.3 + - - -
39B PHE 3.8 2.9 - - - -
41B GLN* 1.4 73.2 - - - +
43B ALA* 1.3 62.0 + - - +
45B HIS* 3.4 2.8 + - - +
46B PHE* 3.0 27.4 + - - +
116B MET* 4.6 0.7 - - - +
118B ASP* 3.8 25.9 + - - +
119B VAL* 3.8 26.9 - - + -
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B MET* 3.9 4.4 - - + +
39B PHE 2.9 18.5 + - - +
40B ILE* 3.7 7.2 - - - +
42B THR* 1.3 76.6 - - - +
44B ALA* 1.3 55.7 + - - +
46B PHE* 3.3 3.5 - - - +
47B ALA 3.0 22.9 + - - -
72B VAL* 3.2 28.4 - - + +
75B VAL* 4.6 5.8 - - + -
82B MET* 3.5 33.6 - - + +
84B ILE* 4.5 0.3 - - - +
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Residues in contact with ALA 44 (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 GLN* 3.7 9.6 - - - +
4B SER* 3.6 33.2 - - - +
7B TYR* 3.5 22.2 - - + +
8B ALA* 4.7 2.7 - - + -
40B ILE 2.9 18.7 + - - +
41B GLN 3.6 4.9 - - - +
42B THR 3.3 0.2 - - - -
43B ALA* 1.3 73.9 - - - +
45B HIS* 1.3 59.8 + - - +
47B ALA 3.3 1.0 + - - -
48B ALA* 3.0 24.4 + - - +
72B VAL* 3.9 6.4 - - - +
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Residues in contact with HIS 45 (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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330A LYS* 5.4 5.8 - - + -
1B MET 5.4 5.8 - - - +
3B GLN* 3.6 26.9 - - + +
41B GLN 3.1 18.0 + - - +
42B THR 3.4 4.9 + - - +
44B ALA* 1.3 72.2 - - - +
46B PHE* 1.3 64.6 + - - +
48B ALA* 3.2 4.0 + - + -
49B GLU* 2.8 51.8 + - + +
54B THR 3.9 2.0 - - - -
55B ASN* 3.6 19.8 - - + -
116B MET* 3.3 16.0 - - + +
118B ASP* 3.0 30.1 + - - +
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Residues in contact with PHE 46 (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 TYR* 3.8 30.1 - + - -
30B MET* 4.9 1.8 - - + -
42B THR* 3.0 15.1 + - + +
43B ALA* 3.3 13.7 - - - +
45B HIS* 1.3 76.3 - - - +
47B ALA* 1.3 57.3 + - - +
49B GLU* 3.4 2.4 + - - +
50B SER* 2.7 34.3 + - - -
82B MET* 3.6 22.2 - - + -
84B ILE* 3.5 17.7 - - + -
113B ASN* 3.3 49.3 - - + +
114B GLN* 4.7 0.2 - - - -
116B MET* 3.7 19.2 - - + +
119B VAL* 4.4 10.8 - - + -
122B ALA* 3.5 26.2 - - + -
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Residues in contact with ALA 47 (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* 4.2 5.8 - - + +
43B ALA 3.0 13.8 + - - +
44B ALA 3.6 8.3 - - - +
45B HIS 3.3 0.2 - - - -
46B PHE* 1.3 76.1 - - - +
48B ALA* 1.3 54.6 + - - +
50B SER* 3.2 8.2 + - - -
51B SER* 2.7 33.2 + - - -
70B ALA* 3.7 27.0 - - - +
72B VAL* 4.0 15.5 - - + -
84B ILE* 4.3 13.5 - - + -
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Residues in contact with ALA 48 (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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169A LYS* 4.5 0.2 - - - -
3B GLN* 4.0 16.8 - - - +
7B TYR* 3.5 40.5 - - + +
44B ALA 3.0 11.5 + - - +
45B HIS 3.2 8.0 + - - +
47B ALA* 1.3 75.7 - - - +
49B GLU* 1.3 60.8 + - - +
50B SER 3.2 0.2 - - - -
51B SER 3.2 8.8 + - - -
52B THR 3.4 0.2 + - - -
53B GLY* 2.8 27.7 + - - +
54B THR 4.2 7.6 - - - +
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Residues in contact with GLU 49 (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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167A LYS* 5.4 0.5 + - - -
169A LYS* 3.4 25.0 + - - +
195A GLU* 4.6 1.2 - - - +
330A LYS* 3.0 38.6 + - - +
331A MET* 5.1 3.9 - - - +
45B HIS* 2.8 50.6 + - + +
46B PHE 3.9 4.3 - - - +
48B ALA* 1.3 74.2 - - - +
50B SER* 1.3 58.6 + - - +
51B SER 3.5 0.7 - - - -
53B GLY 3.9 4.0 - - - +
54B THR* 3.8 13.0 - - - -
55B ASN 3.3 7.4 + - - -
112B ASN* 4.6 17.3 + - + +
113B ASN* 4.9 7.5 + - - +
116B MET* 4.2 20.4 - - + -
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Residues in contact with SER 50 (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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169A LYS* 4.7 0.2 - - - -
46B PHE* 2.7 23.3 + - - -
47B ALA* 3.5 5.2 - - - -
48B ALA 3.2 0.6 - - - -
49B GLU* 1.3 75.4 - - - +
51B SER* 1.4 59.9 + - - -
86B TYR* 3.3 33.6 + - - -
90B LEU* 4.9 0.2 - - - +
108B LEU* 3.2 38.8 - - - +
113B ASN* 2.9 29.3 + - - +
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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