Contacts of the helix formed by residues 60 - 74 (chain B) in PDB entry 4L9T
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 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B ALA* 4.7 0.2 - - - -
59B ARG* 1.3 78.0 - - - +
61B GLY* 1.3 65.0 + - - +
62B PRO* 3.3 24.1 - - - +
63B THR* 3.0 31.0 + - - +
64B VAL* 3.1 11.5 + - - +
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Residues in contact with GLY 61 (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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50B GLN* 3.4 11.4 - - - +
54B ALA* 4.6 8.0 - - - +
59B ARG 4.0 0.2 + - - -
60B THR* 1.3 71.1 - - - +
62B PRO* 1.3 64.1 - - - +
64B VAL* 3.2 5.7 + - - +
65B SER* 2.8 34.6 + - - -
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Residues in contact with PRO 62 (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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60B THR* 3.3 20.6 - - - +
61B GLY* 1.3 89.3 - - - +
63B THR* 1.3 61.2 + - + +
65B SER* 3.4 8.2 + - - +
66B ASN* 3.3 22.3 + - - +
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Residues in contact with THR 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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59B ARG* 3.3 44.3 - - - +
60B THR* 3.0 28.6 + - - +
62B PRO* 1.3 78.8 - - + +
64B VAL* 1.3 61.7 + - - +
66B ASN* 3.5 4.9 + - - +
67B LEU* 3.1 25.7 + - - +
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Residues in contact with VAL 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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50B GLN* 3.6 25.4 - - + +
53B ILE* 3.7 22.7 - - + -
54B ALA* 3.6 26.2 - - + +
57B LEU* 4.6 9.9 - - + -
59B ARG* 4.0 14.1 - - + -
60B THR 3.1 14.9 + - - +
61B GLY* 3.7 6.7 - - - +
63B THR* 1.3 77.8 + - - +
65B SER* 1.3 56.0 + - - +
67B LEU* 3.4 6.6 + - + +
68B LEU* 2.8 40.1 + - + +
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Residues in contact with SER 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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50B GLN* 2.8 35.2 + - - +
61B GLY 2.8 16.8 + - - -
62B PRO* 3.7 7.9 - - - +
63B THR 3.3 0.2 - - - -
64B VAL* 1.3 76.7 - - - +
66B ASN* 1.3 57.4 + - - +
68B LEU* 3.4 3.1 + - - +
69B ARG* 2.8 29.7 + - - +
79B ARG* 4.8 2.7 + - - +
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Residues in contact with ASN 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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62B PRO 3.3 13.0 + - - +
63B THR* 4.0 4.9 - - - +
65B SER* 1.3 77.5 - - - +
67B LEU* 1.3 53.7 + - - +
69B ARG* 3.0 8.5 + - - +
70B ASN* 2.7 41.5 + - - +
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Residues in contact with LEU 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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30B THR* 5.2 0.2 - - - +
32B GLU* 3.5 36.1 - - + +
33B GLN* 3.8 16.8 - - + +
36B THR* 3.2 35.4 - - + +
53B ILE* 6.1 0.2 - - + -
57B LEU* 4.7 4.7 - - + -
63B THR 3.1 17.3 + - - +
64B VAL* 3.6 7.0 - - + +
66B ASN* 1.3 79.5 - - - +
68B LEU* 1.3 57.3 + - + +
70B ASN* 3.2 8.6 + - - +
71B LEU* 2.9 49.8 + - + +
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Residues in contact with LEU 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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36B THR* 4.3 23.1 - - + -
40B LEU* 5.0 1.3 - - + -
50B GLN* 3.7 24.9 - - + +
53B ILE* 4.8 5.4 - - + -
64B VAL* 2.8 42.2 + - + +
65B SER 3.9 1.6 - - - +
67B LEU* 1.3 70.2 - - + +
69B ARG* 1.3 61.2 + - - +
71B LEU* 3.4 1.5 + - + -
72B GLU* 2.8 32.1 + - - +
77B ILE* 3.5 25.5 - - + +
79B ARG* 3.6 19.5 - - - +
91B ILE* 3.8 31.2 - - + -
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Residues in contact with ARG 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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65B SER 2.8 21.4 + - - +
66B ASN* 3.3 11.9 - - - +
68B LEU* 1.3 72.2 - - - +
70B ASN* 1.3 59.0 + - - +
72B GLU* 3.3 3.6 + - - +
73B ARG* 2.9 32.6 + - - +
79B ARG* 4.3 13.8 - - - +
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Residues in contact with ASN 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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33B GLN* 3.1 35.7 + - - +
66B ASN* 2.7 21.3 + - - +
67B LEU* 3.2 11.6 + - - +
69B ARG* 1.3 75.4 - - - +
71B LEU* 1.3 65.6 + - - +
73B ARG* 3.4 40.6 + - - +
74B LYS* 3.4 27.5 + - - +
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Residues in contact with LEU 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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29B ILE* 4.8 2.5 - - + -
33B GLN* 4.0 24.9 - - + +
36B THR* 3.8 15.3 - - + -
37B LEU* 3.8 29.4 - - + -
67B LEU* 2.9 40.9 + - + +
68B LEU* 4.9 0.4 - - + -
70B ASN* 1.3 79.9 - - - +
72B GLU* 1.3 61.1 + - - +
74B LYS* 3.3 7.3 + - + +
75B LYS 3.2 3.1 + - - -
76B LEU* 3.1 47.2 + - + +
77B ILE* 3.8 26.9 - - + -
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Residues in contact with GLU 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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68B LEU 2.8 17.9 + - - +
69B ARG* 3.7 3.8 - - - +
71B LEU* 1.3 75.6 - - - +
73B ARG* 1.3 59.8 + - - +
75B LYS* 2.8 26.8 + - - +
77B ILE* 3.7 24.4 - - + +
78B TYR* 4.9 0.6 - - - -
79B ARG* 2.5 60.7 + - - +
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Residues in contact with ARG 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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69B ARG 2.9 16.1 + - - +
70B ASN* 3.5 36.1 + - - +
71B LEU 3.4 0.2 - - - -
72B GLU* 1.3 76.4 - - - +
74B LYS* 1.3 63.6 + - + +
75B LYS* 3.6 6.1 + - - +
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Residues in contact with LYS 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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27B LEU 4.7 1.0 + - - -
28B ASP* 2.7 53.7 + - - +
29B ILE* 4.3 6.6 - - + +
33B GLN* 5.1 0.6 + - - -
70B ASN* 3.4 24.1 + - - +
71B LEU* 3.3 9.7 + - - +
72B GLU 3.1 0.6 - - - -
73B ARG* 1.3 80.7 - - + +
75B LYS* 1.3 69.6 + - - +
76B LEU* 3.2 29.5 + - + +
96B SER* 4.6 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