Contacts of the helix formed by residues 24 - 37 (chain H) in PDB entry 3G3B
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 24 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18H ASP* 3.4 8.1 - - - -
19H ASN* 3.7 11.5 + - - +
22H GLY 4.1 0.8 + - - -
23H TYR* 1.3 75.7 - - - +
25H LEU* 1.3 67.7 + - - +
27H ASN* 2.9 37.8 + - - +
28H TRP* 3.7 1.6 - - - -
120H VAL* 3.7 8.0 - - - +
121H GLN* 3.2 33.3 + - - +
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Residues in contact with LEU 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9H ALA* 3.4 22.2 - - + +
12H MET* 3.7 16.4 - - + -
13H LYS* 3.6 39.0 - - + +
17H LEU* 4.1 5.2 - - + -
18H ASP* 2.8 39.9 + - - +
23H TYR 3.6 0.6 + - - -
24H SER* 1.3 70.2 - - - +
26H GLY* 1.3 52.4 + - - +
28H TRP* 2.8 35.3 + - + +
29H VAL* 3.3 12.4 + - + +
121H GLN* 3.9 3.2 + - - +
124H ILE* 3.6 28.9 - - + -
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Residues in contact with GLY 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LEU* 1.3 76.4 - - - +
27H ASN* 1.3 60.0 + - - +
28H TRP 3.3 0.2 - - - -
29H VAL* 4.1 2.2 - - - -
30H CYS* 3.1 24.3 + - - +
120H VAL* 3.3 23.8 - - - +
121H GLN* 2.9 20.3 + - - -
123H TRP* 3.9 7.6 - - - +
124H ILE* 3.7 13.7 - - - +
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Residues in contact with ASN 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H TYR* 4.0 15.1 - - + +
24H SER* 2.9 46.7 + - - +
25H LEU 2.9 0.4 + - - -
26H GLY* 1.3 76.5 - - - +
28H TRP* 1.3 59.5 + - + +
30H CYS* 3.6 3.0 - - - +
31H ALA* 3.1 25.5 + - - +
105H MET* 3.4 22.8 - - - +
111H TRP* 3.2 29.7 + - - +
115H CYS 5.1 0.2 - - - +
116H LYS* 5.1 1.7 - - - -
120H VAL* 3.6 22.9 - - - +
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Residues in contact with TRP 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12H MET* 3.7 27.8 - - + +
17H LEU* 3.0 52.9 + - + -
20H TYR* 4.0 28.5 - + - -
23H TYR* 3.5 18.2 + + + +
24H SER 3.7 9.0 - - - -
25H LEU* 2.8 16.4 + - + +
27H ASN* 1.3 77.2 - - + +
29H VAL* 1.3 66.2 + - - +
31H ALA* 2.9 15.3 + - - +
32H ALA 3.0 10.4 + - - -
56H LEU* 4.5 10.0 - - + +
95H ALA* 4.2 22.9 - - + -
99H VAL* 3.6 36.3 - - + -
105H MET* 4.0 24.7 - - + -
108H TRP* 4.4 4.3 - + - -
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Residues in contact with VAL 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5H ARG* 4.0 23.1 - - + +
8H LEU* 4.6 5.2 - - + -
9H ALA* 3.8 32.1 - - + +
12H MET* 3.8 17.7 - - - -
25H LEU* 3.3 11.4 + - + +
26H GLY* 4.2 5.6 - - - +
28H TRP* 1.3 75.6 - - - +
30H CYS* 1.3 64.2 - - - +
32H ALA* 3.2 1.6 + - - +
33H LYS 3.0 18.9 + - - -
38H PHE* 3.5 18.1 - - + -
123H TRP* 3.9 25.1 - - + +
124H ILE* 4.1 7.4 - - + -
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Residues in contact with CYS 30 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H GLY 3.1 18.7 + - - +
27H ASN* 3.6 5.4 - - - +
29H VAL* 1.3 80.7 - - - +
31H ALA* 1.3 60.0 + - - +
33H LYS* 3.4 4.0 - - - +
34H PHE* 3.2 37.7 + - - -
114H ARG 4.9 0.9 - - - -
115H CYS* 2.0 50.7 - - + -
120H VAL* 5.2 1.1 - - + -
123H TRP* 3.2 39.0 - - + +
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Residues in contact with ALA 31 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ASN 3.1 15.5 + - - +
28H TRP* 2.9 10.6 + - - +
30H CYS* 1.3 75.9 - - - +
32H ALA* 1.3 57.7 + - - +
34H PHE* 3.4 4.3 + - - +
35H GLU* 3.0 32.2 + - - +
56H LEU* 3.9 16.2 - - + -
105H MET* 3.7 19.3 - - + -
108H TRP* 5.0 6.7 - - + +
111H TRP* 4.2 19.6 + - + +
115H CYS* 4.1 0.9 - - - -
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Residues in contact with ALA 32 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8H LEU* 3.7 24.7 - - + -
12H MET* 4.5 4.3 - - + -
28H TRP 3.0 10.4 + - - +
29H VAL 3.6 7.2 - - - +
31H ALA* 1.3 73.9 - - - +
33H LYS* 1.3 66.9 + - - +
34H PHE 3.2 0.2 - - - -
36H SER* 3.0 25.8 + - - -
37H ASN 3.2 4.3 + - - -
38H PHE* 3.4 4.6 + - + -
55H ILE* 3.5 27.1 - - + +
56H LEU* 3.8 8.7 - - + +
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E TRP* 4.0 26.3 + - - +
135E PHE* 6.2 1.2 - - - -
140E LEU* 4.5 14.4 - - + -
29H VAL 3.0 8.6 + - - +
30H CYS 3.4 10.8 - - - +
32H ALA* 1.3 74.7 - - - +
34H PHE* 1.3 68.1 + - + +
37H ASN* 2.9 52.9 + - - +
38H PHE* 3.4 41.5 - - + -
123H TRP* 3.6 24.9 - - + -
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Residues in contact with PHE 34 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E PRO 5.3 1.6 - - - -
140E LEU* 3.8 24.7 - - + -
30H CYS* 3.2 29.7 + - - -
31H ALA 4.1 4.3 - - - +
32H ALA 3.2 0.6 - - - -
33H LYS* 1.3 79.4 - - + +
35H GLU* 1.3 68.2 + - - +
37H ASN 4.9 0.2 + - - -
110H ALA* 4.0 24.8 - - + +
111H TRP 5.2 0.4 - - - +
114H ARG* 3.2 64.8 - - + -
115H CYS* 3.7 24.2 - - - -
123H TRP* 4.2 14.4 - + - -
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Residues in contact with GLU 35 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138G LEU* 5.5 1.4 - - - +
31H ALA 3.0 19.6 + - - +
32H ALA 3.3 0.6 + - - -
34H PHE* 1.3 81.0 - - - +
36H SER* 1.3 58.5 - - - +
37H ASN 3.8 0.2 - - - -
42H ALA* 5.2 0.5 - - - +
55H ILE 3.3 17.7 - - - +
56H LEU* 3.7 10.5 - - + +
57H GLN* 3.4 41.7 + - + +
108H TRP* 3.5 37.1 - - + +
109H VAL 5.2 0.3 + - - -
110H ALA* 4.0 21.1 + - - +
111H TRP 5.0 0.5 + - - -
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Residues in contact with SER 36 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H ALA 3.0 6.8 + - - -
35H GLU* 1.3 76.1 - - - +
37H ASN* 1.3 69.3 + - - +
38H PHE 3.5 1.9 + - - -
39H ASN* 3.0 42.3 + - - +
42H ALA* 3.7 17.9 - - - +
54H GLY 3.8 2.5 - - - -
55H ILE* 2.9 32.2 + - - +
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Residues in contact with ASN 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47F THR* 4.0 24.2 - - - +
2H VAL* 4.1 10.4 - - - +
33H LYS* 2.9 56.3 + - - +
34H PHE 4.6 0.2 - - - -
36H SER* 1.3 78.5 - - - +
38H PHE* 1.3 65.7 + - - +
39H ASN* 3.2 6.1 + - - +
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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