Contacts of the helix formed by residues 90 - 102 (chain H) in PDB entry 3AZL
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 90 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44G GLY* 5.0 2.0 - - - -
47G ALA* 3.9 4.5 - - - -
1001G CL 3.6 17.5 - - + -
88H THR* 3.6 24.0 - - + +
89H ILE* 1.3 76.5 - - - +
91H SER* 1.3 66.1 + - - +
92H ARG* 3.0 17.7 + - - +
93H GLU* 2.7 37.4 + - - +
94H ILE* 3.2 11.3 + - - +
186J G 5.8 0.2 - - - +
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Residues in contact with SER 91 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G GLY* 4.0 20.8 - - - -
47G ALA* 4.0 8.7 - - - +
50G TYR* 3.9 23.9 - - - -
1001G CL 3.4 11.8 - - - +
90H THR* 1.3 74.8 + - - +
92H ARG* 1.3 58.5 + - - +
93H GLU 3.3 0.2 - - - -
94H ILE* 3.7 5.8 - - - +
95H GLN* 3.0 29.1 + - - +
118H VAL* 4.7 8.9 - - - +
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Residues in contact with ARG 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74F GLU 3.7 2.0 + - - -
75F HIS* 2.7 57.2 + - + +
77F GLN* 3.4 34.3 + - - +
90H THR* 3.0 13.0 + - - +
91H SER* 1.3 82.0 + - - +
93H GLU* 1.3 65.2 + - - +
95H GLN* 3.5 9.1 + - - +
96H THR* 3.1 25.2 + - - +
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Residues in contact with GLU 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F HIS* 2.8 36.1 + - + +
77H ALA* 3.8 31.1 - - + +
80H LEU* 3.8 8.0 - - + +
81H ALA* 4.2 16.8 - - + +
86H ARG* 5.4 7.6 - - - +
88H THR 3.8 6.5 - - - +
89H ILE* 4.4 3.6 - - + -
90H THR* 2.7 52.8 + - - +
92H ARG* 1.3 82.8 + - - +
94H ILE* 1.3 66.2 + - - +
96H THR 3.4 0.3 + - - -
97H ALA* 3.0 24.8 + - - +
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Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G LEU* 5.0 4.7 - - + -
47G ALA* 3.9 13.5 - - + +
50G TYR* 3.2 35.0 - - + -
51G LEU* 4.1 32.8 - - + +
54G VAL* 4.8 0.4 - - + -
73H ILE* 4.1 16.4 - - + +
74H ALA* 5.7 0.7 - - - -
77H ALA* 4.0 7.2 - - + -
89H ILE* 3.3 32.1 - - + -
90H THR 3.2 9.5 + - - +
91H SER* 3.9 8.5 - - - +
92H ARG 3.4 0.4 - - - -
93H GLU* 1.3 78.1 - - - +
95H GLN* 1.3 56.8 + - - +
97H ALA* 3.3 6.2 - - - +
98H VAL* 3.0 30.5 + - + +
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Residues in contact with GLN 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50G TYR* 2.5 37.7 + - + +
91H SER 3.0 17.7 + - - +
92H ARG* 3.8 10.3 - - - +
94H ILE* 1.3 74.0 - - - +
96H THR* 1.3 67.0 + - - +
97H ALA 3.1 1.3 - - - -
98H VAL* 3.1 5.3 + - - +
99H ARG* 2.9 32.9 + - - +
111H VAL* 3.3 28.0 - - + +
115H THR* 3.4 15.6 - - - +
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Residues in contact with THR 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F THR* 3.9 22.8 - - + +
75F HIS* 2.8 38.8 - - + +
80H LEU* 3.3 31.9 - - + -
92H ARG* 3.1 7.3 + - - +
95H GLN* 1.3 77.8 - - - +
97H ALA* 1.3 57.2 + - - +
99H ARG* 3.2 11.5 + - - +
100H LEU* 2.9 30.6 + - + +
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Residues in contact with ALA 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H ILE* 3.8 28.9 - - + +
76H GLU* 4.0 23.1 - - + -
77H ALA* 4.0 5.4 - - - +
80H LEU* 3.7 1.5 - - + +
93H GLU 3.0 18.9 + - - +
94H ILE* 3.3 8.1 - - - +
96H THR* 1.3 75.0 - - - +
98H VAL* 1.3 59.2 + - - +
100H LEU* 3.2 2.1 + - - +
101H LEU* 2.8 37.1 + - - +
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Residues in contact with VAL 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G TYR* 4.7 1.3 - - + -
54G VAL* 3.9 31.9 - - + -
73H ILE* 4.0 14.8 - - + -
94H ILE* 3.0 23.6 + - + +
95H GLN* 3.1 10.3 + - - +
97H ALA* 1.3 75.0 - - - +
99H ARG* 1.3 59.0 + - - +
101H LEU* 4.6 3.8 - - - -
102H LEU* 2.9 41.7 + - + +
107H ALA* 4.2 12.4 - - - +
110H ALA* 3.8 26.7 - - + -
111H VAL* 4.2 9.0 - - + +
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Residues in contact with ARG 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F THR* 4.8 13.5 - - + -
95H GLN* 2.9 25.8 + - - +
96H THR* 3.2 13.0 + - - +
98H VAL* 1.3 77.7 - - - +
100H LEU* 1.3 59.8 + - - +
101H LEU 3.5 0.2 + - - -
102H LEU 3.7 12.0 - - - +
107H ALA* 4.5 14.4 - - + +
108H LYS* 3.8 34.0 - - - +
111H VAL* 3.6 40.1 - - + +
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Residues in contact with LEU 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68F ASP* 3.8 34.8 - - + +
71F THR* 3.7 30.5 - - + +
72F TYR* 3.9 32.5 - - + +
92F ARG* 3.0 38.6 + - - +
76H GLU* 4.0 17.0 - - + -
80H LEU* 4.3 1.1 - - + -
96H THR* 2.9 32.2 + - + +
97H ALA* 3.8 3.6 - - - +
99H ARG* 1.3 75.8 - - - +
101H LEU* 1.3 59.4 - - - +
102H LEU 5.0 0.2 - - - -
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F ARG* 3.3 21.9 + - - +
96G LEU* 3.9 14.0 - - + +
72H ARG* 3.3 57.1 + - + +
73H ILE* 3.5 18.8 - - + +
76H GLU* 4.2 14.1 - - + +
79H ARG* 6.3 0.2 - - - +
97H ALA 2.8 19.2 + - - +
98H VAL* 4.0 2.5 - - - +
100H LEU* 1.3 80.3 - - - +
102H LEU* 1.3 71.7 + - + +
103H PRO* 3.9 2.4 - - - +
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Residues in contact with LEU 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54G VAL* 4.5 3.6 - - + -
58G LEU* 3.9 33.0 - - + -
96G LEU* 3.5 26.5 - - + -
69H ILE* 5.1 7.2 - - + -
73H ILE* 5.4 2.9 - - + -
98H VAL* 2.9 28.8 + - + +
99H ARG 3.7 13.5 - - - +
100H LEU 5.0 0.3 - - - -
101H LEU* 1.3 81.1 - - + +
103H PRO* 1.3 71.1 - - + +
104H GLY 3.9 0.3 + - - -
106H LEU* 3.8 9.2 - - + +
107H ALA* 3.7 17.1 - - - +
110H ALA* 3.6 31.4 - - + -
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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