Contacts of the helix formed by residues 30 - 42 (chain U) in PDB entry 4GGF
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 TYR 30 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68T THR 2.7 29.0 + - - -
69T ASN* 4.4 9.5 - - + -
70T ALA* 4.8 0.2 - - - +
23U LYS* 3.5 38.4 - - + +
24U GLY* 3.7 7.4 - - - -
25U ASN* 3.0 19.4 + - - +
28U ALA* 3.6 18.2 - - + -
29U VAL* 1.3 75.4 - - - +
31U ARG* 1.3 62.6 + - - +
32U ASP* 3.3 15.5 - - - +
33U ASP* 3.0 25.7 + - - +
34U LEU* 2.8 26.5 + - - +
55U PHE* 3.9 0.9 - - - -
64U GLY 3.6 20.4 - - - +
65U ALA* 3.9 6.1 - - + -
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Residues in contact with ARG 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30U TYR* 1.3 76.2 - - - +
32U ASP* 1.3 61.8 + - - +
34U LEU* 3.3 3.6 + - - +
35U LYS* 3.2 20.8 + - - +
51U ALA* 5.4 3.3 - - + +
52U ASP* 3.2 46.4 + - - +
55U PHE* 3.5 58.5 - - + +
56U LYS* 5.2 1.2 - - - +
64U GLY 4.4 1.2 + - - +
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Residues in contact with ASP 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U LYS* 2.9 35.9 + - - -
30U TYR* 3.7 10.9 - - - +
31U ARG* 1.3 73.2 - - - +
33U ASP* 1.3 68.3 + - - -
35U LYS* 3.4 11.9 + - + +
36U LYS* 3.2 20.6 + - - +
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Residues in contact with ASP 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U TYR* 3.9 25.5 - - + +
22U ILE* 3.7 21.4 - - + +
23U LYS* 2.7 29.4 + - - +
28U ALA 4.2 1.2 - - - +
29U VAL* 3.7 12.3 - - + +
30U TYR* 3.0 40.8 + - - +
32U ASP* 1.3 82.8 + - - +
34U LEU* 1.3 56.8 + - - +
36U LYS* 3.4 8.7 + - - +
37U LEU* 2.9 27.5 + - - +
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29U VAL* 3.4 16.8 - - + +
30U TYR 2.8 12.7 + - - +
31U ARG 3.7 8.1 - - - +
32U ASP 3.2 0.2 - - - -
33U ASP* 1.3 75.1 - - - +
35U LYS* 1.3 60.7 + - - +
37U LEU* 3.1 17.7 + - + +
38U LEU* 2.8 47.3 + - + +
51U ALA 3.9 9.2 - - - +
54U TRP* 4.1 5.8 - - + -
55U PHE* 3.6 45.1 - - + +
58U LEU* 4.3 18.8 - - + -
66U VAL* 4.6 9.2 - - + -
71U PHE* 5.8 0.9 - - + -
74U LEU* 4.7 4.9 - - + -
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Residues in contact with LYS 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31U ARG 3.2 12.8 + - - +
32U ASP* 3.4 14.6 + - + +
34U LEU* 1.3 76.7 - - - +
36U LYS* 1.3 56.4 + - - +
38U LEU* 3.4 2.0 + - - +
39U GLU* 2.7 69.3 + - + +
51U ALA* 3.8 27.9 - - + +
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Residues in contact with LYS 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U TYR* 3.7 15.3 - - + -
22U ILE* 4.2 22.0 - - + -
32U ASP 3.2 10.2 + - - +
33U ASP* 3.5 9.9 - - - +
35U LYS* 1.3 76.0 - - - +
37U LEU* 1.3 65.2 + - - +
39U GLU* 3.3 8.4 + - - -
40U THR* 2.9 36.7 + - - +
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Residues in contact with LEU 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U VAL* 5.2 0.9 - - + +
16U TYR* 5.0 4.9 - - - -
19U TYR* 3.6 43.5 - - + -
29U VAL* 4.7 10.3 - - + -
33U ASP 2.9 14.9 + - - +
34U LEU* 3.1 20.2 + - + +
36U LYS* 1.3 74.9 - - - +
38U LEU* 1.3 62.6 + - + +
41U GLU* 2.8 48.5 + - + +
42U SER* 5.9 1.1 - - - -
71U PHE* 3.9 29.4 - - + -
74U LEU* 4.0 24.9 - - + -
8V LEU* 4.9 2.9 - - + -
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Residues in contact with LEU 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34U LEU* 2.8 29.0 + - + +
35U LYS* 3.8 3.8 - - - +
37U LEU* 1.3 78.5 - - + +
39U GLU* 1.3 62.2 + - + +
42U SER* 2.8 42.2 + - - +
46U ILE* 4.3 4.5 - - + +
47U ARG* 3.4 14.5 - - + +
50U GLY 5.0 0.2 - - - -
51U ALA* 3.7 36.8 - - + +
54U TRP* 3.9 34.3 - - + -
74U LEU* 3.9 32.3 - - + -
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Residues in contact with GLU 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U LYS* 2.7 60.4 + - + +
36U LYS* 3.3 7.5 + - - +
38U LEU* 1.3 78.0 - - + +
40U THR* 1.3 61.0 + - - +
42U SER 4.7 2.1 - - - +
47U ARG* 3.8 30.3 + - - +
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Residues in contact with THR 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U TYR* 3.2 26.1 + - - +
36U LYS* 2.9 26.1 + - - +
39U GLU* 1.3 81.3 - - - +
41U GLU* 1.3 65.0 + - - +
42U SER 3.7 0.9 - - - -
6V SER* 3.4 15.0 - - - -
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Residues in contact with GLU 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U VAL* 3.7 19.7 - - + +
18U LYS* 4.9 6.9 - - - +
19U TYR* 2.5 39.1 + - + +
37U LEU* 2.8 28.3 + - + +
40U THR* 1.3 81.4 - - - +
42U SER* 1.3 58.0 + - - +
78U MET* 3.9 6.6 - - - +
6V SER* 2.8 27.9 + - - -
7V GLN* 3.7 7.6 + - - +
8V LEU* 3.3 40.0 + - + +
9V GLU* 3.6 10.3 - - - +
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Residues in contact with SER 42 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37U LEU* 5.9 0.9 - - - -
38U LEU* 2.8 34.6 + - - +
39U GLU 4.7 2.4 - - - +
40U THR 5.2 0.2 - - - -
41U GLU* 1.3 80.8 - - - +
43U PRO* 1.3 70.1 - - - +
46U ILE* 3.6 23.6 - - - +
47U ARG* 3.1 27.2 + - - +
78U MET* 3.9 11.9 - - - -
9V GLU* 4.2 3.1 - - - -
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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