Contacts of the helix formed by residues 74 - 89 (chain B) in PDB entry 1TLF
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 HIS 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A HIS* 3.6 42.4 + + + -
78A GLN* 6.3 0.4 - - - -
277A GLU* 6.2 2.5 - - + -
278A ASP* 3.0 27.2 + - - -
72B ALA 3.8 8.7 + - - -
73B LEU* 1.3 73.7 - - - +
75B ALA* 1.3 67.3 + - - +
77B SER* 3.3 6.1 + - - -
78B GLN* 2.9 30.4 + - + +
248B GLN* 2.8 42.8 + - + +
276B THR* 3.7 28.7 - - + -
278B ASP* 3.9 14.3 + - - -
282B TYR* 4.6 2.5 - - - -
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Residues in contact with ALA 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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74B HIS* 1.3 75.1 - - - +
76B PRO* 1.3 63.0 - - + +
78B GLN* 2.8 6.0 + - - +
79B ILE* 2.8 38.5 + - - +
248B GLN* 4.8 0.4 + - - -
274B ASP* 4.3 5.2 - - - +
276B THR* 3.9 8.7 - - + +
293B PHE* 3.6 32.3 - - + -
998B IPT 3.6 27.2 + - - +
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Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.0 4.9 - - - +
69B SER* 3.5 30.7 - - - +
70B SER 3.4 23.8 - - - +
71B LEU* 4.1 3.1 - - + -
73B LEU* 3.8 8.1 - - + -
74B HIS 3.7 2.0 - - - -
75B ALA* 1.3 94.3 - - + +
77B SER* 1.3 55.4 + - - +
79B ILE* 3.4 3.4 + - + +
80B VAL* 2.9 35.7 + - - +
125B ASN* 4.0 15.7 - - - +
998B IPT 3.4 25.4 - - - +
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 2.6 25.5 + - - +
72A ALA* 4.5 4.9 - - - -
77A SER* 2.9 12.1 + - - -
71B LEU* 2.5 40.7 + - - +
73B LEU 3.2 4.3 + - - -
74B HIS* 3.3 11.4 + - - -
75B ALA 3.1 0.4 - - - -
76B PRO* 1.3 75.5 - - - +
78B GLN* 1.3 62.6 + - - +
80B VAL* 3.5 1.8 + - - +
81B ALA* 3.0 29.6 + - - +
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Residues in contact with GLN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ALA* 5.2 13.7 - - + +
74B HIS* 2.9 16.1 + - + +
75B ALA 2.8 8.1 + - - +
77B SER* 1.3 76.4 - - - +
79B ILE* 1.3 57.2 + - - +
81B ALA* 3.3 4.4 + - - +
82B ALA* 2.9 31.4 + - - +
275B ASP 4.8 1.7 - - - +
276B THR* 3.1 28.1 - - - +
277B GLU* 3.1 50.0 + - + +
293B PHE* 3.9 24.4 - - + +
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ALA 2.8 23.9 + - - +
76B PRO* 3.8 2.0 - - + +
78B GLN* 1.3 70.8 - - - +
80B VAL* 1.3 58.6 + - + +
82B ALA* 3.5 6.4 - - - +
83B ILE* 2.9 42.6 + - + +
125B ASN* 3.4 28.9 - - + +
148B LEU* 4.1 15.0 - - + -
293B PHE* 3.3 42.4 - - + -
296B LEU* 3.7 28.5 - - + -
297B GLY 5.2 0.7 - - - +
998B IPT 4.0 15.3 - - + -
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LEU* 3.6 16.2 - - + -
98A MET* 3.3 24.3 - - - +
66B VAL* 4.1 19.3 - - + -
68B THR* 3.8 20.9 - - + +
71B LEU* 4.0 8.1 - - + -
76B PRO 2.9 21.5 + - - +
77B SER 3.9 3.6 - - - +
79B ILE* 1.3 76.8 - - + +
81B ALA* 1.3 59.1 + - - +
83B ILE* 3.5 9.5 - - + +
84B LYS* 3.1 24.9 + - - +
94B VAL* 5.7 1.3 - - + +
96B VAL* 3.8 15.9 - - + -
125B ASN* 5.4 1.6 - - - +
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Residues in contact with ALA 81 (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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70A SER* 4.2 16.8 - - - +
72A ALA* 4.4 11.9 - - + +
98A MET* 3.6 18.6 - - + +
77B SER 3.0 19.0 + - - +
78B GLN* 3.3 4.5 + - - +
80B VAL* 1.3 74.3 - - - +
82B ALA* 1.3 66.4 + - - +
84B LYS* 3.3 4.5 + - - +
85B SER* 3.0 23.2 + - - -
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Residues in contact with ALA 82 (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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78B GLN 2.9 17.1 + - - +
79B ILE 3.5 4.5 - - - +
81B ALA* 1.3 74.7 - - - +
83B ILE* 1.3 59.0 + - - +
85B SER* 2.8 32.6 + - - -
86B ARG* 3.3 6.4 + - - +
293B PHE 3.2 30.5 - - - +
294B ARG* 4.0 14.1 - - + +
297B GLY* 4.0 9.2 - - - -
298B GLN 5.0 0.3 + - - -
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Residues in contact with ILE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 5.2 1.1 - - + -
66B VAL* 3.8 40.4 - - + -
79B ILE* 2.9 38.9 + - + +
80B VAL* 3.5 10.5 - - - +
82B ALA* 1.3 77.5 - - - +
84B LYS* 1.3 62.0 + - - +
86B ARG 3.3 1.0 + - - -
87B ALA* 3.1 20.3 + - - +
94B VAL* 4.2 17.7 - - + -
123B ILE* 4.1 25.6 - - + -
125B ASN* 6.0 0.2 - - + -
148B LEU* 4.9 0.9 - - + -
297B GLY* 3.9 16.8 - - - +
300B SER* 5.1 1.3 - - - -
301B VAL* 3.4 23.2 - - + +
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Residues in contact with LYS 84 (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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98A MET* 3.2 48.3 + - + -
99A VAL 4.3 3.6 - - - -
100A GLU* 3.0 34.1 + - + +
80B VAL 3.1 12.6 + - - +
81B ALA 3.5 9.6 - - - +
82B ALA 3.2 0.4 - - - -
83B ILE* 1.3 80.8 - - - +
85B SER* 1.3 62.3 + - - +
87B ALA* 4.3 5.2 - - - -
88B ASP* 2.9 57.3 + - - +
94B VAL* 4.5 13.5 - - + -
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ALA 3.0 13.3 + - - -
82B ALA* 2.8 21.0 + - - -
84B LYS* 1.3 74.5 - - - +
86B ARG* 1.3 64.3 + - - +
88B ASP* 3.2 11.8 + - - +
89B GLN* 3.3 21.1 + - - +
294B ARG* 6.2 3.8 - - - -
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Residues in contact with ARG 86 (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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82B ALA 3.3 3.6 + - - +
83B ILE 3.3 2.5 + - - +
85B SER* 1.3 75.5 - - - +
87B ALA* 1.3 58.1 + - - +
89B GLN* 2.6 60.3 + - - +
90B LEU* 2.8 42.0 + - - +
297B GLY 4.4 0.4 - - - +
298B GLN* 3.0 55.9 + - + +
301B VAL* 3.5 23.1 - - + -
302B ASP* 2.9 28.8 + - - -
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Residues in contact with ALA 87 (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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64B ILE* 4.8 0.4 - - + -
83B ILE 3.1 10.2 + - - +
84B LYS 3.7 3.6 - - - +
86B ARG* 1.3 77.1 - - - +
88B ASP* 1.3 66.9 + - - +
90B LEU 3.3 0.2 + - - -
91B GLY 3.1 5.4 + - - -
92B ALA* 2.7 51.6 + - + -
93B SER* 4.4 0.7 - - - +
94B VAL* 3.4 33.2 - - + -
301B VAL* 3.8 8.9 - - + +
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Residues in contact with ASP 88 (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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100A GLU* 3.3 21.8 - - - +
84B LYS* 2.9 56.6 + - - +
85B SER* 3.5 7.0 - - - +
86B ARG 3.0 1.2 + - - -
87B ALA* 1.3 79.7 - - - +
89B GLN* 1.3 60.6 + - + +
91B GLY* 4.1 6.2 + - - -
92B ALA 5.0 4.7 - - - +
93B SER* 6.0 0.3 - - - -
94B VAL* 5.8 0.2 - - - +
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Residues in contact with GLN 89 (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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85B SER* 3.3 16.1 + - - +
86B ARG* 2.6 47.3 + - - +
88B ASP* 1.3 73.7 - - + +
90B LEU* 1.3 68.2 + - + +
91B GLY 3.2 6.5 + - - -
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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