Contacts of the helix formed by residues 19 - 29 (chain A) in PDB entry 6S6A
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 GLY 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLY 3.2 2.0 - - - -
18A SER* 1.3 78.6 - - - +
20A LYS* 1.3 67.7 + - - +
22A SER* 3.3 2.1 - - - -
23A MET* 3.0 31.4 + - - +
127A HIS* 4.1 2.4 + - - -
401A GTP 2.9 41.3 + - - -
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Residues in contact with LYS 20 (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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12A LEU* 3.6 29.5 - - + +
13A MET* 3.4 16.8 - - - +
14A GLY* 2.9 41.5 + - - +
15A LYS 3.3 5.1 + - - -
18A SER* 3.7 9.0 - - - +
19A GLY* 1.3 77.0 - - - +
21A THR* 1.3 65.9 + - - +
23A MET* 3.2 10.7 + - - +
24A ARG 3.1 16.5 + - - -
62A ASP* 3.8 9.2 - - - +
63A CYS 3.2 24.5 - - - -
65A GLY 3.8 0.8 - - - +
91A VAL* 3.9 14.8 - - + -
401A GTP 2.8 42.2 + - - +
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Residues in contact with THR 21 (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 LYS* 1.3 74.6 - - - +
22A SER* 1.3 58.0 + - - +
24A ARG* 3.6 17.3 - - - +
25A SER* 2.7 39.6 + - - -
39A LEU* 3.9 24.9 - - + -
40A GLY 5.4 2.2 - - - +
42A THR* 2.8 6.1 + - - +
46A GLU* 4.9 2.5 - - - +
62A ASP* 2.5 25.1 + - - +
401A GTP 3.1 9.4 + - - -
402A MG 2.2 30.4 - - - -
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Residues in contact with SER 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 3.3 7.2 - - - -
21A THR* 1.3 73.6 - - - +
23A MET* 1.3 61.1 - - - +
25A SER* 2.7 19.0 + - - -
26A ILE* 3.0 16.1 + - - +
36A THR* 3.2 25.9 - - - +
39A LEU* 3.5 14.9 - - - +
164A ILE* 4.6 2.2 - - - -
401A GTP 2.6 53.5 + - - -
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Residues in contact with MET 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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12A LEU* 4.9 1.1 - - - -
19A GLY 3.0 19.0 + - - +
20A LYS* 3.2 6.9 + - - +
22A SER* 1.3 74.0 - - - +
24A ARG* 1.3 63.4 + - - +
26A ILE* 3.2 2.2 + - - +
27A ILE* 3.0 29.4 + - - +
91A VAL* 3.8 22.7 - - + -
125A LEU* 3.4 35.9 - - + -
127A HIS* 3.3 47.1 - - + +
162A THR* 3.8 2.2 - - - +
164A ILE* 4.8 2.0 - - + -
169A LEU* 4.0 20.4 - - + -
173A TRP* 3.6 27.1 - - + +
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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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12A LEU* 4.5 10.1 - - + -
20A LYS 3.1 9.1 + - - +
21A THR* 3.2 18.8 + - - +
23A MET* 1.3 80.0 - - - +
25A SER* 1.3 59.7 + - - +
28A PHE* 3.0 47.9 + - + +
29A ALA* 3.7 2.1 + - + +
42A THR* 4.9 0.6 + - - -
46A GLU* 2.6 60.2 + - - +
48A SER* 3.5 24.7 - - - -
60A LEU* 4.0 26.8 + - + -
62A ASP* 2.7 33.9 + - - +
173A TRP* 5.3 2.5 - - + -
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Residues in contact with SER 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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21A THR* 2.7 20.9 + - - -
22A SER* 2.7 21.7 + - - -
24A ARG* 1.3 76.2 - - - +
26A ILE* 1.3 53.7 + - - +
29A ALA* 3.2 25.0 + - - +
31A TYR* 3.1 58.2 + - - +
36A THR* 3.9 3.8 - - - +
39A LEU* 4.0 8.9 - - - +
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Residues in contact with ILE 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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22A SER 3.0 17.8 + - - +
23A MET 3.2 4.0 + - - +
25A SER* 1.3 76.6 - - - +
27A ILE* 1.3 65.4 + - - +
30A ASN 4.0 9.0 + - - -
31A TYR* 4.0 25.2 - - + +
32A ILE* 5.6 0.7 - - - -
33A ALA* 4.0 12.1 - - - +
36A THR* 3.9 17.7 - - + -
164A ILE* 3.4 43.7 - - + +
169A LEU* 4.1 16.6 - - + -
170A TYR* 3.6 26.8 + - + +
236A LYS* 4.1 7.6 - - - -
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Residues in contact with ILE 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 MET 3.0 17.0 + - - +
26A ILE* 1.3 75.3 - - - +
28A PHE* 1.3 90.8 + - + +
29A ALA 3.8 0.2 - - - -
30A ASN 5.1 0.2 - - - -
169A LEU* 4.0 20.9 - - + +
170A TYR* 3.6 38.8 - - + -
173A TRP* 4.0 31.4 - - + -
209A ALA 4.8 0.9 - - - +
210A THR* 3.3 25.7 - - + +
212A LEU* 4.2 21.8 - - + -
236A LYS* 4.6 4.0 + - - -
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Residues in contact with PHE 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* 3.0 26.0 + - + +
27A ILE* 1.3 93.8 - - + +
29A ALA* 1.3 59.6 + - - +
30A ASN* 3.8 3.4 + - - -
48A SER* 5.6 0.9 - - - +
50A VAL* 3.6 42.2 - - + +
52A PHE* 4.9 4.5 - + - -
58A LEU* 4.2 19.1 - - + -
60A LEU* 3.6 24.0 - - + -
173A TRP* 3.4 39.7 - + - -
177A VAL* 4.7 5.2 - - + -
210A THR* 3.9 17.5 - - + -
212A LEU* 5.2 0.2 - - + -
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Residues in contact with ALA 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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24A ARG* 3.7 2.2 + - + +
25A SER* 3.2 25.3 + - - +
28A PHE* 1.3 78.8 - - + +
30A ASN* 1.3 79.2 + - - +
31A TYR* 3.3 19.4 + - + -
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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