Contacts of the helix formed by residues 24 - 38 (chain K) in PDB entry 5GAG
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 THR 24 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1140A C 3.7 15.5 - - - +
1141A U 3.6 27.5 + - - +
22K GLY 3.7 2.4 + - - -
23K LYS* 1.3 73.2 - - - +
25K LEU* 1.3 71.5 + - - +
27K ARG* 3.4 22.6 + - + +
28K LEU* 3.1 20.1 + - - +
62K VAL* 4.9 0.2 - - - -
63K ALA* 3.3 10.3 - - - +
64K VAL* 4.7 0.2 - - - -
65K THR* 4.7 15.4 - - + +
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Residues in contact with LEU 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139A G 4.1 21.3 - - - +
1140A C 3.7 6.5 - - - +
23K LYS 3.6 0.2 + - - -
24K THR* 1.3 74.7 - - - +
26K GLY* 1.3 65.3 + - - +
28K LEU* 3.3 5.5 + - + +
29K ALA* 2.9 23.4 + - + +
62K VAL* 4.0 24.2 - - + -
63K ALA 3.0 9.4 + - - +
64K VAL* 3.9 14.6 - - + -
72K LYS* 4.8 2.2 - - - -
74K TYR* 4.1 12.8 - - - +
89K PHE* 4.3 9.0 - - + -
100K VAL* 3.9 31.6 - - + -
101K ILE* 4.6 12.6 - - + -
104K ALA* 4.1 18.2 - - + -
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Residues in contact with GLY 26 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1139A G 3.2 31.0 - - - -
1140A C 3.2 10.7 + - - -
1143A A 3.7 6.5 - - - -
25K LEU* 1.3 80.8 - - - +
27K ARG* 1.3 57.2 + - - +
29K ALA* 2.9 9.8 + - - +
30K THR* 2.9 33.3 + - - +
108K MET* 4.0 0.8 - - - +
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Residues in contact with ARG 27 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A U 2.9 53.1 + - + +
1140A C 3.4 23.3 + - - -
1141A U 3.0 24.1 + - - +
1142A A 4.0 9.8 + - - -
1143A A 2.7 47.1 + - - +
24K THR* 3.4 24.0 + - + +
25K LEU 3.3 0.6 - - - -
26K GLY* 1.3 75.2 - - - +
28K LEU* 1.3 57.8 + - - +
30K THR* 2.9 14.4 + - - -
31K GLU* 4.1 6.9 + - - +
142K ILE 4.8 3.5 - - - +
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Residues in contact with LEU 28 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K VAL* 3.8 29.6 - - + -
20K ALA* 4.0 24.0 - - + -
23K LYS* 4.2 21.8 - - + -
24K THR 3.1 16.0 + - - +
25K LEU* 3.7 6.7 - - + +
27K ARG* 1.3 77.2 - - - +
29K ALA* 1.3 66.0 + - - +
30K THR 3.3 0.2 - - - -
31K GLU* 3.1 8.7 + - - +
32K LEU* 3.0 47.1 + - + +
56K VAL* 5.0 1.6 - - + -
62K VAL* 4.9 9.2 - - + -
101K ILE* 4.6 12.3 - - + -
142K ILE* 4.2 17.0 - - + +
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Residues in contact with ALA 29 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25K LEU* 2.9 16.0 + - + +
26K GLY* 2.9 10.7 + - - +
28K LEU* 1.3 78.1 - - + +
30K THR* 1.3 63.5 + - - +
32K LEU* 3.1 15.0 + - - +
33K ALA* 2.9 23.2 + - - +
101K ILE* 5.6 2.0 - - + +
104K ALA* 4.1 24.9 - - + +
105K VAL* 4.1 7.9 - - + +
108K MET* 4.0 16.8 - - + +
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Residues in contact with THR 30 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A C 3.5 23.8 - - - +
1006A C 4.0 11.1 - - - +
1012A U 2.9 32.8 + - - +
1143A A 3.4 12.6 - - - +
26K GLY 2.9 17.6 + - - +
27K ARG 2.9 11.6 + - - -
29K ALA* 1.3 74.3 - - - +
31K GLU* 1.3 65.7 + - - +
33K ALA* 3.0 4.9 + - - +
34K ARG* 2.9 27.6 + - - +
108K MET* 3.8 24.2 - - + -
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Residues in contact with GLU 31 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1012A U 6.1 3.8 - - + -
27K ARG 4.4 5.6 - - - +
28K LEU 3.1 8.6 + - - +
30K THR* 1.3 79.3 + - - +
32K LEU* 1.3 69.0 + - - +
34K ARG* 2.2 44.8 + - - +
35K ARG* 2.5 52.4 + - - +
142K ILE* 3.2 41.8 - - + +
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Residues in contact with LEU 32 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K VAL* 4.4 11.0 - - + -
28K LEU* 3.0 40.6 + - + +
29K ALA* 3.3 7.6 - - - +
31K GLU* 1.3 75.4 - - - +
33K ALA* 1.3 57.9 + - - +
35K ARG* 3.3 1.6 + - - +
36K LEU* 2.9 35.1 + - - +
54K ILE* 3.7 22.4 - - + +
56K VAL* 3.8 25.6 - - + -
101K ILE* 4.3 8.1 - - + -
105K VAL* 3.9 23.3 - - + -
122K LEU* 4.4 6.3 - - + -
140K LEU* 6.0 0.7 - - + -
142K ILE* 4.3 18.8 - - + -
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Residues in contact with ALA 33 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006A C 3.7 24.2 - - - +
29K ALA 2.9 12.7 + - - +
30K THR* 3.3 9.6 - - - +
32K LEU* 1.3 78.3 - - - +
34K ARG* 1.3 58.3 + - - +
36K LEU* 3.3 3.7 + - - +
37K ARG* 3.0 33.1 + - - +
105K VAL* 4.9 3.8 - - + +
108K MET* 4.2 12.1 - - + -
109K LEU* 4.2 22.5 - - + +
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Residues in contact with ARG 34 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005A C 5.5 0.2 - - - -
1006A C 3.9 38.6 - - - +
30K THR 2.9 12.5 + - - +
31K GLU* 2.2 47.8 + - - +
33K ALA* 1.3 78.4 - - - +
35K ARG* 1.3 68.2 + - - +
38K GLY 3.4 2.1 + - - -
39K LYS* 3.1 59.1 + - + +
40K HIS* 3.3 38.2 + - - +
67R ALA* 6.3 0.4 - - - +
70R ARG* 5.4 13.3 - - - +
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Residues in contact with ARG 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K TYR* 5.0 10.1 + - - -
31K GLU* 2.5 39.6 + - - +
32K LEU* 4.1 2.7 - - - +
34K ARG* 1.3 87.1 - - - +
36K LEU* 1.3 61.1 + - - +
37K ARG 3.4 0.2 - - - -
38K GLY 3.8 1.7 + - - +
40K HIS* 3.4 45.3 + - + +
51K GLY* 3.4 4.0 - - - -
52K ASP* 2.9 29.6 + - + +
54K ILE* 4.2 13.5 - - + -
140K LEU* 4.0 32.7 - - - +
142K ILE* 3.6 23.3 - - - +
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Residues in contact with LEU 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K LEU 2.9 22.2 + - - +
33K ALA* 3.3 5.6 + - - +
35K ARG* 1.3 76.1 - - - +
37K ARG* 1.3 64.7 + - - +
49K ASP* 3.3 19.6 - - - +
51K GLY* 3.7 2.3 - - - -
52K ASP 3.7 17.9 - - - +
54K ILE* 4.0 8.1 - - + -
105K VAL* 3.9 25.6 - - + -
109K LEU* 4.4 14.1 - - + -
118K MET* 3.5 28.6 - - + +
119K PHE* 5.2 0.2 - - - -
121K LYS* 3.4 30.4 + - + +
122K LEU* 3.9 24.5 - - + +
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Residues in contact with ARG 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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559A G 6.2 0.2 - - - -
1006A C 5.4 0.2 - - - -
1007A C 2.9 43.9 + - - -
1008A A 2.9 38.8 + - - -
1009A A 4.2 1.4 + - - -
33K ALA 3.0 17.1 + - - +
34K ARG* 4.4 0.4 - - - +
36K LEU* 1.3 80.2 - - - +
38K GLY* 1.3 56.8 + - - +
39K LYS* 4.0 22.0 - - + +
44K TYR* 3.5 29.7 + - + -
46K PRO* 4.9 11.1 + - - +
48K VAL 4.6 1.2 - - - +
50K THR* 3.1 18.2 + - - -
51K GLY* 4.2 1.1 - - - -
109K LEU* 5.1 2.2 - - + -
110K PRO* 3.6 25.7 - - - +
118K MET* 3.6 28.6 - - + +
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Residues in contact with GLY 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34K ARG 3.4 4.6 + - - -
35K ARG 3.8 0.6 + - - -
36K LEU 3.3 3.0 - - - -
37K ARG* 1.3 80.9 - - - +
39K LYS* 1.3 58.4 + - - +
40K HIS* 3.0 21.6 + - - -
41K LYS* 3.4 18.2 + - - +
44K TYR* 3.7 7.8 - - - +
50K THR* 3.3 17.8 + - - -
51K GLY* 3.7 15.7 - - - -
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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