Contacts of the helix formed by residues 38 - 50 (chain A) in PDB entry 4TKR
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.3 28.6 - - - +
22A LEU* 4.2 5.4 - - - +
23A SER* 4.9 0.8 + - - +
36A SER* 3.0 3.8 + - - -
37A LEU* 1.3 75.9 - - - +
39A MET* 1.3 59.4 + - - +
40A ILE 3.2 1.1 - - - -
41A PRO* 3.2 17.8 - - - +
42A MET* 3.3 10.4 - - - +
61A TRP* 3.4 24.8 - - - -
301A TPP 5.1 1.0 + - - -
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Residues in contact with MET 39 (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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36A SER* 3.5 15.7 - - - +
37A LEU 3.1 0.8 - - - -
38A GLY* 1.3 76.9 - - - +
40A ILE* 1.3 54.9 + - - +
42A MET* 3.1 5.3 + - + +
43A TYR* 2.7 75.6 + - + +
61A TRP* 3.7 12.8 - - - -
90A ILE* 4.0 22.4 - - + -
93A SER* 4.4 2.2 - - - +
123A GLY 4.7 8.3 - - - +
124A GLY* 4.8 4.0 - - - -
127A ARG* 3.0 43.3 - - - +
128A TYR* 5.3 1.3 - - + -
164A THR* 3.6 15.0 - - + -
168A SER* 4.0 9.0 - - - +
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Residues in contact with ILE 40 (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 LEU* 4.8 5.6 - - + -
37A LEU* 3.5 25.1 - - + +
38A GLY 3.2 0.2 - - - -
39A MET* 1.3 77.7 - - - +
41A PRO* 1.3 68.7 - - + +
43A TYR* 3.3 11.8 + - - -
44A VAL* 3.3 17.0 + - + +
167A VAL 4.7 0.2 - - - +
168A SER* 3.6 27.1 - - - +
171A ILE* 3.6 46.0 - - + -
172A ILE* 3.8 17.0 - - + +
175A LEU* 4.6 8.7 - - + -
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Residues in contact with PRO 41 (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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15A PHE* 3.3 37.1 - - + +
18A VAL* 3.7 26.0 - - + -
19A ALA* 3.7 9.6 - - + +
22A LEU* 3.7 11.4 - - + -
37A LEU 3.6 4.7 - - - +
38A GLY 3.2 15.0 - - - +
40A ILE* 1.3 96.3 - - + +
42A MET* 1.3 60.0 + - - +
44A VAL* 3.2 21.7 - - + +
45A ILE* 3.2 13.9 - - - +
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Residues in contact with MET 42 (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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15A PHE* 3.4 33.9 - - + +
16A ALA* 3.9 10.1 - - - +
19A ALA* 3.9 7.4 - - + -
38A GLY 3.3 13.7 - - - +
39A MET* 3.1 14.7 + - + +
41A PRO* 1.3 80.8 - - - +
43A TYR* 1.3 58.5 + - - +
45A ILE* 3.2 6.0 - - + +
46A ALA* 3.1 29.6 + - - +
54A ALA* 4.6 3.6 - - - +
57A ALA* 3.9 16.8 - - + +
58A GLY* 3.6 30.3 - - - -
61A TRP* 3.6 21.1 - - + -
90A ILE* 3.8 22.4 - - + -
93A SER* 4.8 0.5 - - - -
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Residues in contact with TYR 43 (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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39A MET* 2.7 47.1 + - + +
40A ILE 3.3 0.4 + - - +
41A PRO 3.3 0.2 - - - -
42A MET* 1.3 73.8 - - - +
44A VAL* 1.3 66.1 + - - +
46A ALA* 3.3 3.8 + - - +
47A ILE* 3.0 30.3 + - + +
93A SER* 3.6 29.6 - - - -
120A MET* 2.8 66.1 + - + -
124A GLY* 4.0 1.8 - - - -
164A THR* 5.5 0.5 - - - +
165A VAL* 3.7 19.5 - - - +
168A SER* 3.6 29.2 - - - -
169A GLY 4.7 0.9 - - - -
172A ILE* 3.7 20.9 - - + -
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Residues in contact with VAL 44 (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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15A PHE* 3.5 26.0 - - + -
40A ILE* 3.3 14.7 + - + +
41A PRO* 3.2 22.0 - - + +
43A TYR* 1.3 76.2 - - - +
45A ILE* 1.3 49.7 - - - +
47A ILE* 3.1 3.1 + - - +
48A ARG* 2.6 39.5 + - + +
172A ILE* 4.1 3.5 - - + +
175A LEU* 6.0 2.2 - - + -
182A LEU* 3.9 34.5 - - + +
183A PHE* 3.6 34.7 - - + -
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Residues in contact with ILE 45 (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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11A GLU* 4.0 18.4 - - + +
12A CYS* 4.4 21.3 - - - +
15A PHE* 3.6 34.8 - - + -
41A PRO 3.2 13.2 - - - +
42A MET* 3.2 18.4 - - - +
44A VAL* 1.3 81.0 - - - +
46A ALA* 1.3 59.5 + - - +
48A ARG* 4.2 4.7 - - - -
49A ARG* 2.9 51.3 + - + +
50A GLY 3.6 2.1 + - - +
53A ALA* 4.6 3.4 - - + +
54A ALA* 4.7 7.0 - - - -
57A ALA* 4.3 17.5 - - + -
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Residues in contact with ALA 46 (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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42A MET 3.1 20.2 + - - +
43A TYR 3.5 5.8 - - - +
44A VAL 3.1 0.2 - - - -
45A ILE* 1.3 77.7 - - - +
47A ILE* 1.3 51.9 + - - +
50A GLY* 3.0 17.8 + - - -
54A ALA* 3.6 25.6 - - + -
93A SER* 3.6 31.0 - - - +
94A GLY 3.9 0.2 - - - +
97A SER* 2.2 26.2 + - - -
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Residues in contact with ILE 47 (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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43A TYR* 3.0 16.4 + - + +
44A VAL 3.6 5.8 - - - +
46A ALA* 1.3 78.3 - - + +
48A ARG* 1.3 55.9 + - - +
49A ARG 3.5 0.5 + - - -
93A SER 5.1 0.4 - - - +
97A SER* 3.4 12.8 - - - +
100A VAL* 3.7 38.1 - - + -
101A ARG* 2.7 39.5 + - + +
116A ALA* 4.5 9.9 - - + -
119A THR* 4.7 16.6 - - + -
120A MET* 5.6 1.8 - - + -
172A ILE* 4.3 16.8 - - + -
176A LEU* 4.8 0.9 - - + -
183A PHE* 3.9 37.2 - - + -
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Residues in contact with ARG 48 (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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11A GLU* 2.8 39.0 + - - -
15A PHE* 4.5 17.8 - - - -
44A VAL 2.6 21.9 + - - +
45A ILE* 4.2 4.3 - - - +
47A ILE* 1.3 74.1 - - - +
49A ARG* 1.3 65.4 + - + +
101A ARG* 3.7 8.9 + - - -
181A LYS 3.6 14.6 + - - -
182A LEU* 3.1 31.4 + - - +
183A PHE* 3.5 13.0 - - - +
185A PRO* 3.5 52.5 - - + +
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Residues in contact with ARG 49 (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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7A ILE* 4.2 10.7 - - - +
8A ILE* 3.7 41.9 - - + +
11A GLU* 2.9 35.7 + - + +
45A ILE* 2.9 32.5 + - + +
48A ARG* 1.3 87.7 - - + +
50A GLY* 1.3 61.2 + - - +
52A TRP* 4.8 9.9 + - - -
53A ALA* 3.5 20.3 - - + +
101A ARG* 4.7 7.7 + - - -
185A PRO* 3.5 31.3 - - - +
302A BGL 5.4 0.7 + - - -
304B BGL 5.5 4.7 + - - -
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Residues in contact with GLY 50 (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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45A ILE 3.6 0.6 + - - -
46A ALA* 3.0 21.3 + - - +
47A ILE 4.4 0.6 + - - -
48A ARG 3.9 0.2 - - - -
49A ARG* 1.3 80.3 - - - +
51A PHE* 1.3 65.7 + - - -
52A TRP* 3.6 2.2 - - - -
53A ALA* 3.6 2.4 + - - +
54A ALA* 3.2 23.7 + - - +
94A GLY* 4.3 2.7 - - - -
97A SER* 3.7 12.8 - - - -
101A ARG* 4.9 0.4 - - - -
302A BGL 4.1 8.5 - - - -
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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