Contacts of the helix formed by residues 22 - 33 (chain A) in PDB entry 4HFG
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 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A SER* 4.1 2.9 - - - -
18A ASN 3.3 8.4 + - - -
19A SER 2.9 21.6 + - - -
20A GLN 3.5 0.4 - - - -
21A HIS* 1.3 82.3 - - - +
23A VAL* 1.3 62.9 + - - +
24A GLN* 3.7 3.3 + - - -
25A THR* 3.1 18.0 + - - -
26A LEU* 3.0 22.9 + - - +
16B LEU* 5.2 0.2 - - - -
58B THR* 4.4 12.3 - - - -
61B TYR* 4.0 12.4 - - - -
202B SO4 3.1 23.6 - - - -
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Residues in contact with VAL 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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21A HIS 3.9 0.2 + - - -
22A SER* 1.3 71.1 - - - +
24A GLN* 1.3 56.4 + - - +
26A LEU* 3.5 0.6 + - - -
27A SER* 2.9 27.4 + - - -
58A THR* 3.6 35.9 - - + +
61A TYR* 3.9 13.0 - - + +
62A LEU* 3.6 30.3 - - + +
65A ASP* 4.1 9.4 - - + +
16B LEU* 3.9 17.2 - - + +
22B SER* 5.4 0.2 - - - -
23B VAL* 6.3 0.4 - - + -
24B GLN* 4.0 11.4 - - - +
202B SO4 2.7 28.3 + - - +
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Residues in contact with GLN 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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22A SER* 3.1 2.4 + - - +
23A VAL* 1.3 79.4 - - - +
25A THR* 1.3 63.9 - - - +
27A SER* 2.8 31.2 + - - -
28A LEU* 3.1 25.3 + - - +
65A ASP* 3.3 27.1 + - - +
69A ASN* 4.1 11.8 + - - +
204A UNX 4.3 5.1 - - - -
23B VAL* 6.6 0.4 - - + -
61B TYR* 3.0 54.9 + - + +
64B ASN* 4.3 14.1 - - - +
110B ILE* 6.0 1.9 - - - +
202B SO4 4.2 1.0 + - - +
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Residues in contact with THR 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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19A SER 2.6 26.9 + - - +
20A GLN* 3.5 22.4 - - - +
22A SER* 3.1 11.6 + - - -
24A GLN* 1.3 74.1 - - - +
26A LEU* 1.3 66.0 + - - +
28A LEU* 3.2 22.5 + - + +
29A TRP* 3.3 13.1 + - + +
57B LEU* 4.7 3.8 - - - +
61B TYR* 3.9 13.3 + - - -
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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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20A GLN 5.0 1.4 + - - -
21A HIS 5.8 0.7 - - - +
22A SER 3.0 15.8 + - - +
23A VAL* 3.8 5.6 - - - +
25A THR* 1.3 77.4 - - - +
27A SER* 1.3 60.6 + - - +
29A TRP* 3.1 18.8 + - + +
30A LEU* 3.0 30.3 + - + +
62A LEU* 3.8 29.2 - - + -
9B LEU* 4.5 2.5 - - + -
12B LYS* 3.8 46.0 - - + +
13B LEU* 3.9 16.6 - - + -
16B LEU* 4.0 14.6 - - + -
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Residues in contact with SER 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 VAL 2.9 16.4 + - - -
24A GLN* 2.8 20.4 + - - -
25A THR 3.2 0.2 - - - -
26A LEU* 1.3 74.8 - - - +
28A LEU* 1.3 56.5 + - - +
30A LEU* 3.4 2.2 + - - +
31A ILE* 2.9 39.3 + - - +
62A LEU* 3.9 2.4 - - - +
65A ASP* 2.9 31.8 + - - -
66A VAL* 3.9 28.7 - - - +
69A ASN* 5.0 0.2 + - - -
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Residues in contact with LEU 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 GLN* 3.1 28.4 + - - +
25A THR* 3.4 13.5 - - + +
27A SER* 1.3 83.6 + - - +
29A TRP* 1.3 57.4 + - - +
31A ILE* 3.5 8.0 + - + +
32A HIS* 3.0 28.2 + - - +
69A ASN* 6.6 0.2 - - + -
201A SO4 4.9 1.6 + - - -
61B TYR* 3.9 19.3 - - - +
103B PRO* 4.1 23.3 - - + +
106B ARG* 3.6 40.0 + - + +
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Residues in contact with TRP 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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25A THR* 3.3 8.2 + - + +
26A LEU* 3.1 13.0 + - + +
28A LEU* 1.3 78.6 - - - +
30A LEU* 1.3 92.2 + - + +
32A HIS* 3.3 13.1 - + - +
33A HIS* 3.1 49.2 + + - -
3B SER 3.8 23.1 + - - +
4B PHE* 3.7 26.5 - + - -
5B SER 4.4 0.2 - - - -
8B ALA* 4.3 7.0 - - + -
9B LEU* 4.3 16.6 - - + -
12B LYS* 3.7 40.4 - - + +
206B UNX 3.7 20.8 - - - -
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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* 3.0 33.1 + - + +
27A SER* 3.8 4.0 - - - +
28A LEU 3.2 0.2 - - - -
29A TRP* 1.3 97.5 - - + +
31A ILE* 1.3 60.5 + - - +
33A HIS* 2.9 18.4 + - - +
34A ARG 3.1 9.7 + - - -
40A ILE* 3.8 34.3 - - + -
44A TRP* 6.1 1.1 - - + -
62A LEU* 4.2 13.0 - - + -
66A VAL* 4.1 22.7 - - + -
77A PHE* 3.2 20.4 - - + -
81A PHE* 6.2 2.2 - - + -
9B LEU* 3.7 22.2 - - + -
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Residues in contact with ILE 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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24A GLN* 6.1 0.2 - - - +
27A SER* 2.9 29.0 + - - +
28A LEU* 4.0 9.2 - - + +
30A LEU* 1.3 71.3 - - - +
32A HIS* 1.3 68.1 + - - +
34A ARG* 2.9 31.0 + - - +
66A VAL* 4.1 16.6 - - + +
69A ASN* 3.9 34.5 - - + +
70A SER* 4.1 19.1 - - - +
73A LYS* 3.7 32.3 - - + -
77A PHE* 3.9 7.0 - - - -
201A SO4 3.8 8.3 - - - +
106B ARG* 4.2 11.7 - - - +
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Residues in contact with HIS 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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28A LEU 3.0 14.3 + - - +
29A TRP* 3.3 15.7 - + - +
31A ILE* 1.3 81.3 - - - +
33A HIS* 1.3 86.6 + + - +
34A ARG* 3.3 10.2 + - - +
35A LYS* 4.9 0.9 + - - +
201A SO4 2.8 35.7 + - - +
205A UNX 4.1 4.7 - - - -
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Residues in contact with HIS 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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29A TRP* 3.1 58.3 + + - +
30A LEU* 2.9 9.5 + - - +
32A HIS* 1.3 95.9 - + - +
34A ARG* 1.3 52.9 + - - +
35A LYS 3.2 2.9 - - - -
36A HIS* 2.8 37.8 + - + +
40A ILE* 3.5 13.8 - - + +
205A UNX 2.9 26.3 - - - -
3B SER* 4.0 8.1 + - - -
4B PHE* 3.6 34.3 + + + +
205B UNX 3.7 4.9 - - - -
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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