Contacts of the helix formed by residues 69 - 83 (chain A) in PDB entry 1TJY
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 SER 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35A LYS 4.6 0.6 + - - -
65A PRO* 4.7 1.1 - - - +
67A GLU* 3.3 12.7 + - - +
68A PRO* 1.3 77.1 - - - +
70A VAL* 1.3 65.1 + - - +
71A SER* 3.6 6.2 + - - -
72A GLY* 3.0 21.3 + - - -
73A GLN* 3.2 25.3 + - - +
93A VAL* 3.7 10.6 - - - +
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Residues in contact with VAL 70 (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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69A SER* 1.3 73.2 - - - +
71A SER* 1.3 60.5 + - - +
73A GLN* 3.2 2.6 + - - +
74A VAL* 2.8 41.1 + - + +
93A VAL* 4.0 9.0 - - + -
94A SER* 4.0 27.8 - - - +
97A GLY* 3.7 30.3 - - - +
98A LEU* 4.8 3.1 - - + -
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Residues in contact with SER 71 (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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69A SER* 3.4 6.4 + - - -
70A VAL* 1.3 79.2 - - - +
72A GLY* 1.3 63.2 + - - +
74A VAL* 4.1 5.6 - - - +
75A GLN* 3.0 26.2 + - - +
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Residues in contact with GLY 72 (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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65A PRO* 3.9 23.5 - - - +
69A SER* 3.0 19.5 + - - -
70A VAL 3.2 0.2 - - - -
71A SER* 1.3 78.8 - - - +
73A GLN* 1.3 60.8 + - - +
75A GLN* 4.1 3.3 - - - +
76A LEU* 3.5 24.3 + - - +
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Residues in contact with GLN 73 (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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33A ILE* 4.5 5.7 - - + +
34A PRO 3.0 17.3 - - - +
35A LYS* 3.5 2.6 - - - -
65A PRO* 4.3 15.5 - - + -
69A SER 3.2 12.7 + - - +
70A VAL 3.2 4.1 + - - +
72A GLY* 1.3 74.6 - - - +
74A VAL* 1.3 67.2 + - - +
76A LEU* 3.2 9.8 + - - +
77A VAL* 3.0 27.2 + - - +
90A VAL* 3.8 9.3 - - + +
91A SER 2.8 20.8 - - - +
92A ALA* 3.6 1.2 - - - +
93A VAL* 3.0 44.0 - - + +
98A LEU* 3.5 26.4 - - + +
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Residues in contact with VAL 74 (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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70A VAL* 2.8 29.6 + - + +
71A SER* 4.1 5.6 - - - +
73A GLN* 1.3 73.5 - - - +
75A GLN* 1.3 67.1 + - - +
77A VAL* 3.3 6.3 + - - +
78A ASN* 2.9 38.1 + - - +
97A GLY 3.6 24.0 - - - +
98A LEU* 4.1 15.3 - - + -
101A ALA* 4.1 11.4 - - + -
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Residues in contact with GLN 75 (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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71A SER 3.0 18.2 + - - +
72A GLY* 4.1 3.8 - - - +
74A VAL* 1.3 78.3 - - - +
76A LEU* 1.3 62.2 + - + +
78A ASN* 3.3 5.8 + - + +
79A ASN* 2.8 64.2 + - - +
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Residues in contact with LEU 76 (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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33A ILE* 4.1 17.0 - - + -
63A ASP* 3.5 31.6 - - - +
64A GLY* 3.4 39.0 - - - -
65A PRO* 4.0 4.7 - - + -
72A GLY 3.5 16.0 + - - +
73A GLN 3.2 8.1 + - - +
75A GLN* 1.3 81.8 - - + +
77A VAL* 1.3 63.4 + - - +
79A ASN* 3.3 14.3 + - + +
80A PHE* 2.9 42.4 + - + -
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Residues in contact with VAL 77 (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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33A ILE* 4.1 16.4 - - + -
73A GLN 3.0 20.0 + - - +
74A VAL* 3.7 7.0 - - - +
76A LEU* 1.3 77.5 - - - +
78A ASN* 1.3 63.2 + - - +
80A PHE 3.3 0.3 + - - -
81A VAL* 3.0 26.5 + - + +
88A ILE* 3.8 20.2 - - + +
90A VAL* 5.1 2.5 - - + -
98A LEU* 4.8 12.6 - - + -
101A ALA* 3.8 31.0 - - + +
102A LEU* 3.8 31.0 - - + -
105A ALA* 4.8 0.9 - - + -
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Residues in contact with ASN 78 (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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74A VAL* 2.9 35.9 + - - +
75A GLN* 3.8 5.4 - - + +
77A VAL* 1.3 76.2 - - - +
79A ASN* 1.3 60.0 + - - +
81A VAL* 3.3 4.8 + - - +
82A ASN* 2.8 43.5 + - - +
101A ALA* 3.6 24.7 + - - +
104A ARG* 3.7 24.7 - - - +
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Residues in contact with ASN 79 (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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75A GLN* 2.8 61.2 + - - +
76A LEU* 3.6 15.3 - - + +
78A ASN* 1.3 74.7 - - - +
80A PHE* 1.3 61.2 + - + +
82A ASN* 3.2 6.9 + - - +
83A GLN* 2.9 51.5 + - - +
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Residues in contact with PHE 80 (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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31A ALA* 3.4 23.1 - - + -
33A ILE* 4.1 19.7 - - + -
61A THR* 3.9 20.4 - - + -
63A ASP* 4.1 16.8 - - + -
76A LEU* 2.9 44.8 + - + +
77A VAL* 4.8 0.2 - - - -
79A ASN* 1.3 78.5 - - + +
81A VAL* 1.3 63.7 + - - +
83A GLN* 3.4 8.6 + - - -
84A GLY 3.3 4.2 + - - -
85A TYR* 3.0 74.5 + + + +
88A ILE* 3.8 19.3 - - + -
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Residues in contact with VAL 81 (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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77A VAL* 3.0 25.4 + - + +
78A ASN* 3.7 5.2 - - - +
80A PHE* 1.3 76.4 - - - +
82A ASN* 1.3 62.0 + - - +
84A GLY* 3.1 14.2 + - - -
85A TYR 4.4 0.2 + - - -
88A ILE* 3.7 11.7 - - + -
101A ALA 4.8 1.1 - - - +
104A ARG* 3.6 21.5 - - - +
105A ALA* 3.4 37.7 - - + +
108A ARG* 3.9 27.8 + - - +
110A VAL* 4.4 16.4 - - + +
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Residues in contact with ASN 82 (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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78A ASN* 2.8 28.4 + - - +
79A ASN* 3.7 7.7 + - - +
81A VAL* 1.3 75.7 - - - +
83A GLN* 1.3 60.0 - - + +
84A GLY 3.2 1.4 + - - -
104A ARG* 2.9 42.5 + - - +
108A ARG* 3.7 10.0 - - - +
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Residues in contact with GLN 83 (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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29A ARG* 2.9 23.3 + - - +
79A ASN* 2.9 39.5 + - - +
80A PHE* 3.9 11.2 - - - +
81A VAL 3.2 0.4 - - - -
82A ASN* 1.3 76.7 - - + +
84A GLY* 1.3 57.8 + - - +
85A TYR* 3.5 23.6 + - + -
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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