Contacts of the helix formed by residues 22 - 33 (chain A) in PDB entry 5H4G
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 MET 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.0 33.4 - - + +
17A MET* 3.4 15.9 - - - +
19A SER* 3.0 16.5 + - - +
20A GLN 3.3 0.2 - - - -
21A ASN* 1.3 87.6 - - + +
23A LYS* 1.3 65.1 + - - +
24A ARG 3.2 3.1 - - - -
25A ILE* 2.9 50.1 + - + +
26A LEU* 3.0 10.6 + - - +
137A ILE* 4.0 31.2 - - + -
141A GLU* 5.9 0.4 - - - +
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Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER 3.6 6.1 + - - +
20A GLN* 3.2 19.6 + - - +
21A ASN 3.3 2.4 + - - +
22A MET* 1.3 76.2 - - - +
24A ARG* 1.3 64.2 + - - +
26A LEU* 3.3 7.4 + - - +
27A GLU* 2.7 62.4 + - + +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ASN 5.0 1.0 + - - -
22A MET 3.0 1.4 + - - -
23A LYS* 1.3 82.1 - - - +
25A ILE* 1.3 64.6 + - + +
27A GLU* 3.4 17.9 + - - +
28A VAL* 3.4 24.5 + - + +
144A VAL* 4.5 26.0 - - + -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 4.0 18.2 - - + -
22A MET* 2.9 39.9 + - + +
24A ARG* 1.3 76.1 - - + +
26A LEU* 1.3 56.9 + - - +
28A VAL* 3.5 0.7 + - - -
29A THR* 2.7 36.3 + - - +
137A ILE* 4.3 9.0 - - + +
140A VAL* 3.6 33.1 - - + +
141A GLU* 3.5 37.9 - - + +
144A VAL* 4.3 8.3 - - + -
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Residues in contact with LEU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 5.7 2.2 - - + -
17A MET* 3.6 43.7 - - + +
18A HIS* 3.5 35.0 - - + +
19A SER 5.5 2.0 - - - +
22A MET 3.0 7.0 + - - +
23A LYS* 3.7 10.5 - - - +
25A ILE* 1.3 78.3 - - - +
27A GLU* 1.3 60.5 + - + +
29A THR* 3.1 8.3 + - + -
30A LEU* 2.8 50.5 + - + +
66A ILE* 5.2 0.4 - - + -
67A TYR* 3.6 17.7 - - + +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LYS* 2.7 61.6 + - + +
24A ARG* 3.7 23.3 - - - +
25A ILE 3.3 0.2 - - - -
26A LEU* 1.3 76.9 - - + +
28A VAL* 1.3 60.2 + - + +
30A LEU* 3.4 6.5 + - - +
31A ALA* 3.0 28.3 + - - +
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Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 3.4 17.1 + - + +
25A ILE 3.9 0.9 - - - +
26A LEU 3.2 0.2 - - - -
27A GLU* 1.3 76.5 - - + +
29A THR* 1.3 68.5 + - - +
31A ALA* 3.0 14.6 + - + +
32A LYS* 3.1 21.7 + - + +
140A VAL* 3.7 23.8 - - + +
143A MET* 4.0 29.4 - - + -
144A VAL* 4.1 16.4 - - + -
147A GLU* 4.0 26.5 - - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.0 14.6 - - + -
9A PHE* 4.2 10.1 - - + -
17A MET* 3.5 14.4 - - + +
25A ILE 2.7 24.3 + - - -
26A LEU* 3.1 11.4 + - + -
28A VAL* 1.3 77.5 - - - +
30A LEU* 1.3 58.1 + - - +
32A LYS 3.3 0.7 + - - -
33A PHE* 2.9 39.7 + - + +
35A VAL* 4.3 9.6 - - + -
136A PHE* 3.7 30.2 - - + -
140A VAL* 3.8 7.4 - - - +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LEU* 2.8 41.1 + - + +
27A GLU* 4.0 5.8 - - - +
29A THR* 1.3 76.2 - - + +
31A ALA* 1.3 61.9 + - - +
32A LYS 3.4 0.2 + - - -
33A PHE 3.6 13.2 - - - +
35A VAL* 4.1 15.9 - - + +
66A ILE* 3.7 44.6 - - + +
67A TYR* 3.7 27.8 - - + +
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Residues in contact with ALA 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A GLU 3.0 18.1 + - - +
28A VAL* 3.0 9.6 + - + +
30A LEU* 1.3 77.1 - - - +
32A LYS* 1.3 65.3 + - + +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A PRO* 4.8 4.9 - - - +
28A VAL* 3.1 27.5 + - + +
31A ALA* 1.3 86.7 - - + +
33A PHE* 1.3 82.6 + - + +
143A MET* 3.7 34.5 + - + +
147A GLU* 5.1 8.2 + - - +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A LEU* 3.6 43.1 - - + -
4A PRO 3.2 27.8 - - - -
5A PRO* 3.5 7.0 - - + +
7A ILE* 3.9 28.9 - - + -
29A THR* 2.9 28.4 + - + +
30A LEU* 3.6 17.3 - - - +
31A ALA 3.8 0.2 - - - -
32A LYS* 1.3 95.8 - - + +
34A THR* 1.3 61.1 + - - +
35A VAL* 3.9 5.0 + - + +
136A PHE* 4.0 20.4 - + - -
140A VAL* 4.9 2.5 - - + -
143A MET* 4.3 16.6 - - + -
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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