Contacts of the helix formed by residues 83 - 103 (chain B) in PDB entry 4TZM
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 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63B GLU* 5.0 7.9 + - - +
64B TYR* 3.1 32.8 - - + -
80B SER* 3.5 15.7 + - - +
81B PHE 3.4 0.2 - - - -
82B LYS* 1.3 78.9 - - - +
84B LEU* 1.3 57.2 + - - +
85B ARG* 3.1 10.7 + - - +
86B ALA* 3.1 26.8 + - + -
87B HIS* 2.7 37.4 + - - +
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LYS 3.8 4.6 + - - +
83B ASN* 1.3 73.4 + - - +
85B ARG* 1.3 58.0 + - - +
87B HIS* 3.5 15.1 - - + +
88B GLN* 3.0 30.4 + - - +
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Residues in contact with ARG 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 5.1 6.1 - - + +
64B TYR* 3.7 24.0 - - + +
83B ASN* 3.1 10.9 + - - +
84B LEU* 1.3 80.6 - - - +
86B ALA* 1.3 60.9 + - - +
88B GLN* 3.5 15.1 + - - +
89B ILE* 3.5 34.2 + - + +
494D THR* 2.6 31.9 + - - +
495D SER 2.9 29.7 + - - -
496D ILE* 3.7 20.1 - - - +
497D ASN* 5.1 1.6 + - - +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 5.5 0.4 - - + -
64B TYR* 3.5 33.9 - - + +
79B LEU* 4.1 16.8 - - + +
80B SER 3.5 18.2 - - - +
83B ASN* 3.1 16.0 + - + +
85B ARG* 1.3 74.3 - - - +
87B HIS* 1.3 65.1 + - - +
89B ILE* 3.2 8.5 + - - +
90B ALA* 3.1 22.9 + - - +
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Residues in contact with HIS 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER 3.6 5.1 + - - -
81B PHE* 3.3 51.6 + + + +
83B ASN 2.7 22.8 + - - +
84B LEU* 3.3 19.3 + - + +
86B ALA* 1.3 71.8 - - - +
88B GLN* 1.3 63.5 + - - +
90B ALA* 3.3 6.5 + - - +
91B GLN* 3.1 41.4 + - + +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU 3.0 17.6 + - - +
85B ARG* 3.6 20.0 + - - +
87B HIS* 1.3 77.6 - - - +
89B ILE* 1.3 61.6 + - + +
91B GLN* 3.1 19.4 + - + +
92B LEU* 3.2 15.7 + - + +
493D ASN* 5.1 8.3 - - - +
494D THR* 4.0 31.6 + - + +
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Residues in contact with ILE 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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54B LEU* 4.0 7.6 - - + -
60B LEU* 3.5 31.2 - - + -
79B LEU* 3.8 16.8 - - + -
85B ARG* 3.5 29.8 + - - +
86B ALA* 3.2 8.4 + - - +
88B GLN* 1.3 77.4 - - + +
90B ALA* 1.3 63.0 + - - +
92B LEU* 3.2 25.2 + - + +
93B LEU* 3.3 12.9 + - + +
197B PHE* 3.9 28.0 - - + -
494D THR* 5.5 2.5 - - + -
496D ILE* 3.6 22.0 - - + -
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Residues in contact with ALA 90 (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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47B TYR* 4.0 18.0 - - + -
79B LEU* 3.9 11.8 - - + +
81B PHE* 3.8 31.8 - - + -
86B ALA 3.1 12.1 + - - +
87B HIS* 3.5 10.1 - - - +
89B ILE* 1.3 77.7 - - - +
91B GLN* 1.3 51.7 + - - +
93B LEU* 3.1 9.4 + - - +
94B ARG* 2.8 33.5 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PHE* 5.1 4.5 - - - -
87B HIS* 3.1 40.0 + - + +
88B GLN* 3.1 12.5 + - + +
90B ALA* 1.3 74.8 - - - +
92B LEU* 1.3 58.9 + - + +
94B ARG* 3.7 11.7 - - - +
95B ALA* 3.0 30.3 + - - +
212B ASP 4.9 0.8 - - - +
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Residues in contact with LEU 92 (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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88B GLN* 3.2 13.0 + - + +
89B ILE* 3.2 17.4 + - + +
91B GLN* 1.3 77.1 - - - +
93B LEU* 1.3 65.6 + - + +
95B ALA* 4.0 0.5 - - - +
96B ALA* 3.1 19.4 + - - +
197B PHE* 4.7 13.7 - - + -
212B ASP 4.2 2.9 - - - +
213B GLY* 3.5 41.7 - - - +
214B PHE* 3.5 30.5 - - + -
492D SER* 4.0 19.1 - - - -
493D ASN* 4.0 4.5 - - - +
494D THR* 4.0 24.7 - - + +
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE 5.2 2.8 - - - +
46B ILE* 3.9 22.4 - - + +
47B TYR* 4.2 25.4 - - + +
50B PHE* 4.1 19.7 - - + -
51B SER 4.8 0.7 - - - +
54B LEU* 5.4 0.2 - - + -
79B LEU* 4.0 26.7 - - + -
89B ILE* 3.5 11.4 - - + +
90B ALA* 3.1 9.7 + - - +
92B LEU* 1.3 75.5 - - + +
94B ARG* 1.3 60.0 + - - +
96B ALA* 3.5 4.1 + - - +
97B GLY* 2.9 24.6 + - - -
108B ILE* 4.1 15.3 - - + -
197B PHE* 3.7 35.2 - - + -
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Residues in contact with ARG 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ILE* 3.9 24.9 - - - +
47B TYR* 6.1 0.6 - - - +
90B ALA 2.8 16.3 + - - +
91B GLN* 3.3 15.9 + - - +
93B LEU* 1.3 78.3 - - - +
95B ALA* 1.3 56.9 + - - +
97B GLY* 3.2 2.3 + - - -
98B ASP* 2.9 60.8 + - - +
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Residues in contact with ALA 95 (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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91B GLN 3.0 17.4 + - - +
92B LEU 4.0 2.0 - - - +
94B ARG* 1.3 75.0 - - - +
96B ALA* 1.3 65.5 + - - +
98B ASP* 3.1 20.8 + - - +
99B ALA* 3.2 9.9 + - - +
211B ILE* 3.6 17.2 - - + +
212B ASP* 3.6 35.0 - - + +
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ILE* 4.5 1.6 - - + -
92B LEU 3.1 19.1 + - - +
93B LEU 3.7 4.0 - - - +
95B ALA* 1.3 76.0 - - - +
97B GLY* 1.3 62.6 + - - +
99B ALA* 3.2 14.1 + - - +
100B THR 3.5 2.3 + - - -
105B LEU* 3.3 29.4 - - + +
108B ILE* 3.6 28.9 - - + -
199B LEU* 4.4 11.7 - - + -
211B ILE* 3.8 9.6 - - - +
214B PHE* 4.6 0.2 - - + -
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Residues in contact with GLY 97 (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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43B ILE* 3.3 24.5 - - - +
46B ILE* 3.7 21.9 - - - +
93B LEU 2.9 13.8 + - - -
94B ARG 3.2 4.2 + - - -
96B ALA* 1.3 78.9 - - - +
98B ASP* 1.3 59.9 + - - +
100B THR* 2.8 24.5 + - - -
101B LYS 3.4 1.9 + - - -
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Residues in contact with ASP 98 (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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43B ILE* 3.7 13.1 - - - +
94B ARG* 2.9 51.0 + - - +
95B ALA* 3.1 14.2 + - - +
97B GLY* 1.3 76.0 - - - +
99B ALA* 1.3 61.3 + - - +
101B LYS* 3.2 17.0 + - - +
102B ASP* 3.1 21.2 + - - +
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Residues in contact with ALA 99 (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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95B ALA 3.2 5.5 + - - +
96B ALA 3.4 10.8 - - - +
97B GLY 3.2 0.6 - - - -
98B ASP* 1.3 74.7 - - - +
100B THR* 1.3 59.7 + - - +
102B ASP* 3.1 11.3 + - - +
103B GLY 2.8 22.5 + - - -
104B PHE 2.8 11.9 + - - -
105B LEU* 3.9 13.0 - - + +
209B PHE* 4.4 11.4 - - + -
211B ILE* 3.6 34.8 - - + -
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Residues in contact with THR 100 (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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39B SER* 4.2 13.9 + - - -
42B MET* 4.2 10.1 - - - +
46B ILE* 4.1 14.4 - - + -
96B ALA 3.5 14.8 - - - +
97B GLY* 2.8 15.0 + - - +
99B ALA* 1.3 72.6 - - - +
101B LYS* 1.3 67.0 + - - +
103B GLY* 3.0 9.0 + - - -
105B LEU* 3.6 22.9 - - + -
129B PHE* 4.3 14.6 - - + -
131B TYR* 3.2 33.6 - - - +
240B HIS* 3.9 12.0 + - - -
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Residues in contact with LYS 101 (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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158A GLN* 5.4 5.2 - - - +
36B ASP* 3.8 23.3 - - - +
39B SER* 3.3 33.0 - - - +
40B ASN* 2.2 34.5 + - - +
43B ILE* 4.4 12.3 - - + +
97B GLY 3.4 3.8 + - - +
98B ASP* 3.2 16.7 + - - +
100B THR* 1.3 83.5 + - - +
102B ASP* 1.3 62.9 + - - +
103B GLY 3.6 0.2 + - - -
240B HIS* 5.2 0.9 + - - -
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Residues in contact with ASP 102 (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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137A VAL* 3.9 24.5 - - + +
138A VAL* 4.7 7.3 - - - +
160A ARG* 2.9 26.9 + - - -
98B ASP* 3.1 20.3 + - - +
99B ALA* 3.1 11.2 + - - +
101B LYS* 1.3 78.5 - - - +
103B GLY* 1.3 58.6 + - - +
104B PHE* 3.5 22.8 + - + -
209B PHE* 4.5 7.6 - - - -
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Residues in contact with GLY 103 (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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160A ARG* 3.9 8.7 + - - -
99B ALA 2.8 6.1 + - - -
100B THR 3.0 15.2 + - - -
101B LYS 3.3 0.2 - - - -
102B ASP* 1.3 78.9 - - - +
104B PHE* 1.3 60.9 + - - -
105B LEU 3.6 1.8 - - - -
131B TYR* 3.6 23.7 - - - -
140B ARG* 4.3 9.1 + - - -
202B THR* 3.3 17.2 + - - +
204B ASP* 4.7 2.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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