Contacts of the helix formed by residues 62 - 75 (chain B) 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 ASN 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B GLY* 1.3 65.2 - - - -
63B ASN* 1.3 58.8 + - - +
64B GLU* 2.9 9.5 + - - +
65B ARG* 3.1 53.8 + - - +
66B ILE* 4.0 12.0 + - - +
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Residues in contact with ASN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A PRO* 6.1 0.2 - - - +
23B TYR* 3.6 31.3 - - + -
26B ASP* 3.5 32.8 + - - +
61B GLY* 2.6 11.3 + - - +
62B ASN* 1.3 73.5 - - - +
64B GLU* 1.3 55.2 + - - +
66B ILE* 3.3 13.9 + - - +
67B ILE* 2.9 37.6 + - + +
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Residues in contact with GLU 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER* 3.8 17.8 + - - +
58B ALA 3.9 3.1 - - - +
59B ASN* 3.7 13.6 + - - +
60B THR* 3.2 36.0 + - - +
61B GLY 2.9 12.2 + - - +
62B ASN* 4.6 1.8 - - - -
63B ASN* 1.3 78.0 - - - +
65B ARG* 1.3 60.3 + - + +
67B ILE* 3.2 7.4 + - - +
68B ASN* 2.8 54.9 + - - +
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 5.3 11.9 - - - -
68A HIS* 5.5 4.9 + - - -
127A ALA* 6.2 2.0 - - - +
62B ASN* 3.1 42.9 + - - +
63B ASN 3.4 0.2 - - - -
64B GLU* 1.3 81.7 - - + +
66B ILE* 1.3 63.7 + - + +
68B ASN* 3.7 6.8 + - - +
69B VAL* 3.3 28.6 + - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ASP* 5.5 0.2 - - - +
126A PRO* 3.9 18.8 - - + +
127A ALA* 3.7 39.0 - - + +
129A TYR* 5.4 2.9 - - + -
19B GLN* 4.4 10.5 - - - +
23B TYR* 3.9 33.9 - - + +
62B ASN* 4.2 12.3 - - - +
63B ASN* 3.3 15.8 + - - +
64B GLU 3.3 0.2 - - - -
65B ARG* 1.3 79.3 - - + +
67B ILE* 1.3 65.8 + - - +
69B VAL* 3.3 8.8 + - - +
70B SER* 3.3 19.8 + - - -
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.5 13.0 - - + -
23B TYR* 3.6 33.9 - - + +
26B ASP* 3.6 32.1 - - + +
27B LEU* 3.8 10.8 - - + -
57B SER* 3.6 27.8 - - - -
60B THR* 5.8 0.2 - - - +
63B ASN* 2.9 25.1 + - + +
64B GLU* 3.6 4.7 - - - +
66B ILE* 1.3 76.6 - - - +
68B ASN* 1.3 57.7 + - - +
70B SER* 3.0 4.7 + - - -
71B ILE* 2.9 45.7 + - + +
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LYS* 5.9 1.0 - - - +
57B SER* 3.4 19.1 + - - -
64B GLU* 2.8 47.4 + - - +
65B ARG* 4.1 6.9 - - - +
67B ILE* 1.3 73.0 - - - +
69B VAL* 1.3 61.3 + - - +
71B ILE* 4.2 9.7 - - - +
72B LYS* 3.2 43.8 + - - +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A PHE* 4.4 11.7 - - + +
68A HIS* 3.7 37.0 - - + +
129A TYR* 6.1 1.3 - - + +
130A MET* 5.1 6.3 - - + -
65B ARG 3.3 15.4 + - - +
66B ILE* 3.5 11.2 - - - +
67B ILE 3.1 0.6 - - - -
68B ASN* 1.3 77.4 - - + +
70B SER* 1.3 65.0 + - - +
72B LYS* 3.5 12.5 + - + +
73B LYS* 3.3 48.3 + - - +
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Residues in contact with SER 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A TYR* 3.5 9.5 + - - -
16B ILE* 3.8 14.9 - - - +
19B GLN* 2.3 34.9 + - - -
20B LEU* 3.7 15.7 - - - -
66B ILE 3.3 5.7 + - - -
67B ILE 3.0 8.3 + - - -
69B VAL* 1.3 79.9 - - - +
71B ILE* 1.3 63.4 + - - +
73B LYS* 3.2 9.0 + - - +
74B LEU* 3.1 28.2 + - - +
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Residues in contact with ILE 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 4.5 13.2 - - + -
27B LEU* 4.4 5.2 - - + -
55B LEU* 3.6 36.1 - - + +
56B LYS* 4.0 15.3 - - - +
57B SER 4.1 2.0 - - - +
67B ILE* 2.9 39.4 + - + +
68B ASN* 4.2 9.6 - - - +
70B SER* 1.3 73.6 - - - +
72B LYS* 1.3 67.1 + - + +
74B LEU* 3.2 17.2 + - + +
75B LYS* 3.3 30.9 + - + +
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Residues in contact with LYS 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ASP* 5.3 11.9 - - - -
42A GLU* 5.6 6.5 - - - +
68B ASN* 3.2 35.1 + - - +
69B VAL* 3.6 10.9 - - + +
71B ILE* 1.3 79.8 - - + +
73B LYS* 1.3 62.1 + - + +
75B LYS* 3.2 18.1 + - - +
76B ARG* 3.5 16.4 + - - +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TYR* 4.4 1.0 + - - -
67A PHE 2.9 21.9 + - - -
68A HIS 3.2 26.0 - - - +
69A PHE 3.3 13.0 + - - -
70A MET* 3.6 33.4 - - + +
129A TYR* 4.7 5.8 + - - +
130A MET* 3.7 21.6 - - - +
9B ARG* 4.8 0.3 + - - -
12B GLN* 5.5 2.2 - - - +
13B LEU* 4.1 7.1 - - - +
16B ILE* 3.7 24.7 - - + +
69B VAL* 3.3 24.1 + - + +
70B SER* 3.2 10.8 + - - +
72B LYS* 1.3 76.9 - - + +
74B LEU* 1.3 61.2 + - - +
76B ARG* 3.2 25.9 + - - +
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B LEU* 4.1 22.1 - - + +
16B ILE* 3.8 20.0 - - + -
17B VAL* 4.0 24.0 - - + -
20B LEU* 3.6 29.2 - - + -
47B PHE* 5.2 0.3 - - - -
51B GLN* 2.9 29.6 + - - +
55B LEU* 4.2 15.9 - - + -
70B SER 3.1 16.0 + - - +
71B ILE* 3.4 14.4 - - + +
72B LYS 3.2 0.4 - - - -
73B LYS* 1.3 76.9 - - - +
75B LYS* 1.3 64.0 + - + +
76B ARG 4.1 0.3 - - - +
108B LEU* 5.5 0.4 - - + -
111B PHE* 4.4 21.2 - - + -
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Residues in contact with LYS 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A GLU* 4.4 1.2 - - - +
50B PHE 5.3 0.2 - - - -
51B GLN* 3.2 39.6 + - - +
52B LYS* 4.6 5.0 + - - +
53B ALA 3.2 20.9 + - - -
54B GLN* 5.1 1.6 - - - +
55B LEU* 4.9 8.4 + - - +
71B ILE* 3.3 31.9 - - + +
72B LYS* 3.2 8.9 + - - +
73B LYS 3.2 1.0 - - - -
74B LEU* 1.3 80.3 - - + +
76B ARG* 1.3 63.7 + - - +
77B LYS* 3.6 1.9 + - - -
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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