Contacts of the helix formed by residues 42 - 53 (chain D) in PDB entry 3TGX
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 CYS 42 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A PRO 4.4 7.6 - - - -
188A GLY* 4.6 1.1 - - - -
38D VAL* 3.8 12.8 - - + -
39D GLU* 3.1 38.5 + - + +
41D ASN* 1.3 81.8 - - - +
43D GLU* 1.3 59.6 + - - +
44D TRP 3.2 2.7 - - - +
45D SER* 3.2 3.4 + - - +
46D ALA* 2.8 29.6 + - - +
93D CYS* 2.0 54.1 - - + -
94D PRO* 3.9 3.4 - - + -
99D TYR* 4.7 0.9 - - - +
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Residues in contact with GLU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D VAL* 4.5 2.9 - - + -
39D GLU 3.9 3.8 - - - +
40D THR* 2.8 40.0 - - - +
41D ASN* 3.6 3.0 - - - -
42D CYS* 1.3 72.4 + - - +
44D TRP* 1.3 57.0 + - + +
46D ALA* 3.3 3.1 + - - +
47D PHE* 2.7 37.1 + - - +
114D LEU* 4.0 14.1 - - + +
117D LYS* 4.0 14.5 + - + +
118D MET* 3.9 28.4 - - + +
121D GLN* 2.8 41.6 + - - +
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Residues in contact with TRP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D HIS* 3.3 35.9 - + - -
10D MET* 5.0 2.7 - - - -
41D ASN 5.1 3.0 + - - +
42D CYS* 3.2 0.6 - - - +
43D GLU* 1.3 81.6 - - + +
45D SER* 1.3 63.7 + - - +
47D PHE* 3.6 35.2 - + - +
48D SER* 3.2 22.3 + - - -
77D LYS* 5.9 4.5 - - - -
78D PRO* 4.0 19.5 - - + -
81D THR* 3.7 13.2 - - + -
85D ARG* 3.5 48.6 - - + +
118D MET* 3.5 21.6 - - + +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D CYS* 3.2 6.3 + - - +
44D TRP* 1.3 77.0 - - - +
46D ALA* 1.3 64.1 + - - +
48D SER* 3.2 9.1 + - - -
49D CYS* 3.2 18.2 + - - +
91D LEU* 4.3 16.0 + - - +
93D CYS* 3.6 37.0 + - - +
94D PRO 4.0 11.4 + - - -
99D TYR* 5.2 2.0 - - - -
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Residues in contact with ALA 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D PRO* 3.9 21.9 - - + +
38D VAL* 3.7 23.1 - - + -
42D CYS 2.8 17.0 + - - +
43D GLU 3.7 3.6 - - - +
45D SER* 1.3 73.9 - - - +
47D PHE* 1.3 66.1 + - - +
49D CYS* 3.0 18.3 + - - +
50D PHE* 3.2 18.4 + - - -
99D TYR* 3.9 8.9 + - - +
114D LEU* 3.8 7.2 - - + -
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Residues in contact with PHE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D MET* 4.8 3.8 - - - -
13D LEU* 3.8 23.6 - - + -
43D GLU 2.7 22.1 + - - +
44D TRP* 3.6 28.0 - + - +
46D ALA* 1.3 74.4 - - - +
48D SER* 1.3 63.3 + - - +
49D CYS 3.3 0.3 + - - -
50D PHE* 3.3 6.7 + - - +
51D GLN* 3.2 55.9 + - + +
78D PRO* 3.8 28.7 - - + -
111D PHE* 4.0 20.2 - + - -
114D LEU* 3.4 12.7 - - + +
115D LEU* 3.9 17.3 - - + -
118D MET* 4.0 13.9 - - + -
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D TRP 3.2 11.6 + - - -
45D SER* 3.2 11.0 + - - -
47D PHE* 1.3 80.6 - - - +
49D CYS* 1.3 57.9 + - - +
50D PHE 3.4 0.2 - - - -
51D GLN* 3.7 16.2 + - - +
52D LYS* 2.9 45.4 + - - +
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Residues in contact with CYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO* 3.7 18.4 - - - -
35D PRO* 4.2 7.9 - - + -
45D SER 3.2 10.3 + - - +
46D ALA* 3.0 13.6 + - - +
48D SER* 1.3 76.2 - - - +
50D PHE* 1.3 64.5 + - - +
52D LYS* 3.8 2.4 - - - -
53D ALA* 3.0 25.3 + - - +
96D CYS* 1.9 59.8 - - + -
99D TYR* 4.3 10.1 - - + -
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D PRO 5.0 0.4 + - - -
34D ALA* 4.1 8.1 - - - -
35D PRO* 3.6 44.6 - - + -
46D ALA 3.2 18.9 + - - -
47D PHE 3.5 5.8 - - - +
49D CYS* 1.3 78.9 - - - +
51D GLN* 1.3 61.9 + - - +
53D ALA* 3.3 16.1 - - - +
55D LEU* 5.8 0.7 - - - +
107D PHE* 3.5 36.9 - + - -
110D ARG* 3.6 18.4 - - + -
111D PHE* 3.5 53.3 - + + -
114D LEU* 3.3 34.5 - - + -
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Residues in contact with GLN 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D PHE* 3.2 49.1 + - + +
48D SER* 3.7 14.7 + - - +
49D CYS 3.2 0.2 - - - -
50D PHE* 1.3 81.4 - - - +
52D LYS* 1.3 61.7 + - + +
53D ALA 3.2 5.0 + - - +
74D LEU* 2.9 32.1 + - - +
75D LYS* 3.2 38.2 + - - +
76D ARG 3.0 27.1 + - - -
77D LYS* 4.5 1.1 - - - +
78D PRO* 4.2 3.0 - - - +
111D PHE* 4.7 6.7 - - + -
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D SER* 2.9 33.3 + - - +
49D CYS* 3.8 3.8 - - - +
51D GLN* 1.3 73.5 - - + +
53D ALA* 1.3 66.8 + - - +
54D GLN* 3.6 11.8 + - - +
75D LYS* 4.6 3.6 + - - +
96D CYS* 6.1 2.5 - - - -
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Residues in contact with ALA 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D LEU* 4.5 9.4 - - + -
33D PRO* 4.6 12.1 - - + -
49D CYS 3.0 13.8 + - - +
50D PHE 3.3 16.4 - - - +
51D GLN 3.1 2.6 - - - +
52D LYS* 1.3 81.3 - - - +
54D GLN* 1.3 59.0 + - - +
55D LEU* 3.0 12.8 + - + +
75D LYS* 3.3 17.2 + - - -
96D CYS* 6.1 0.2 - - - -
107D PHE* 3.6 26.9 - - + -
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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