Contacts of the helix formed by residues 81 - 94 (chain A) in PDB entry 1ORZ
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ALA* 4.3 2.2 - - - -
80A ASP* 1.4 98.9 + - - +
82A TRP* 1.3 66.9 + - + +
83A LYS* 2.8 18.2 + - - +
84A TRP* 2.8 71.1 + - - +
85A HIS 3.7 1.2 + - - -
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Residues in contact with TRP 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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73A ALA* 4.5 7.9 - - + +
81A ASN* 1.3 75.6 - - + +
83A LYS* 1.3 81.2 + - + +
85A HIS* 2.7 19.4 + - - -
86A MET* 2.9 11.2 + - + +
103A HIS* 3.7 24.9 - + - -
106A THR* 3.0 40.5 - - + +
107A ARG* 3.5 58.0 - - + +
110A PRO* 5.8 6.5 - - + -
603A PRO* 5.9 0.6 - - - +
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Residues in contact with LYS 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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81A ASN* 2.8 21.3 + - + +
82A TRP* 1.3 86.8 - - + +
84A TRP* 1.3 71.0 + - + +
86A MET* 2.7 51.7 + - + +
87A TYR* 2.9 22.8 + - - +
603A PRO* 5.7 8.3 - - + -
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Residues in contact with TRP 84 (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 HIS* 5.4 3.4 - + - -
79A LYS* 4.6 20.4 - - + -
80A ASP* 3.0 25.6 - - - -
81A ASN* 2.8 47.9 + - - +
82A TRP 3.1 0.2 - - - -
83A LYS* 1.3 94.4 - - + +
85A HIS* 1.3 57.1 + - - +
87A TYR* 3.2 7.9 + - + +
88A ASP* 2.9 33.4 + - - +
148A GLN* 3.3 37.9 - - - +
149A ALA* 6.1 1.8 - - + -
151A ARG* 3.1 20.2 - - - +
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Residues in contact with HIS 85 (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 ASN* 3.1 40.8 + - - -
72A ALA* 5.3 1.8 - - - -
73A ALA* 5.2 5.6 + - + -
80A ASP* 5.2 0.2 - - - +
81A ASN 3.7 1.6 + - - +
82A TRP* 2.7 17.0 + - - +
84A TRP* 1.3 79.6 - - - +
86A MET* 1.3 56.3 + - - +
88A ASP* 5.1 2.2 - - + -
89A THR* 2.7 35.2 + - + +
105A MET* 5.1 4.0 - - + -
106A THR* 3.1 33.4 + - + +
109A ALA* 5.5 0.4 - - - +
147A ALA* 5.7 0.4 - - + -
151A ARG* 3.7 21.7 - - - +
417A LEU* 4.4 4.6 - - + +
420A ASN* 3.3 31.9 + - - -
423A LEU* 4.3 10.2 - - + +
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Residues in contact with MET 86 (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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82A TRP* 2.9 10.7 + - + +
83A LYS* 2.7 48.2 + - + +
85A HIS* 1.3 71.9 - - - +
87A TYR* 1.3 53.0 + - + +
89A THR* 3.1 10.1 + - - +
90A VAL* 2.6 42.2 + - + +
99A GLN* 5.4 2.7 - - - +
102A ILE* 4.2 16.6 - - + -
103A HIS* 3.6 33.9 - - - +
106A THR* 4.2 6.0 + - - +
601A GLU* 3.9 27.4 - - - +
603A PRO* 4.2 13.2 - - + -
604A SER 5.2 2.7 - - - +
605A VAL* 5.5 5.4 - - + -
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Residues in contact with TYR 87 (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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83A LYS* 2.9 21.1 + - - +
84A TRP* 3.8 8.7 - - - +
86A MET* 1.3 79.3 - - + +
88A ASP* 1.3 79.6 + - - +
90A VAL* 3.7 5.2 - - + -
91A LYS* 3.1 60.1 + - + +
95A TRP* 4.2 24.5 - + - -
148A GLN* 5.4 5.4 - - + -
605A VAL* 5.2 5.8 - - + -
608A THR* 4.9 8.6 - - + +
612A TYR* 5.8 0.2 - - - -
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Residues in contact with ASP 88 (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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84A TRP 2.9 13.6 + - - +
85A HIS* 3.8 3.8 - - + +
87A TYR* 1.3 92.5 - - - +
89A THR* 1.3 57.8 + - - +
92A GLY* 3.2 19.6 + - - -
146A GLY* 2.7 30.5 - - - +
147A ALA* 3.9 1.3 - - + -
148A GLN* 3.4 23.8 + - - +
151A ARG* 2.7 40.6 + - - +
417A LEU* 4.7 3.8 - - + +
612A TYR* 3.6 15.3 + - - -
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Residues in contact with THR 89 (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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85A HIS* 2.7 37.6 + - + +
86A MET* 3.3 7.2 - - - +
88A ASP* 1.3 77.0 - - - +
90A VAL* 1.3 58.5 + - - +
92A GLY* 2.9 3.9 + - - +
93A SER* 2.8 29.3 + - - -
102A ILE* 3.7 36.7 - - + +
105A MET* 6.3 1.3 - - + -
106A THR* 4.5 3.8 - - - +
411A VAL* 4.5 2.1 + - - +
412A HIS* 5.6 1.6 - - - -
415A ASN 5.5 1.4 + - - -
417A LEU* 4.2 12.6 + - - +
420A ASN* 3.7 22.9 + - - +
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Residues in contact with VAL 90 (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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86A MET* 2.6 31.5 + - + +
87A TYR* 3.6 11.4 - - - +
89A THR* 1.3 71.1 - - - +
91A LYS* 1.3 63.7 + - - +
93A SER* 2.9 7.3 + - - +
94A ASP 2.9 17.3 + - - -
95A TRP* 3.0 44.6 + - + -
97A GLY 4.3 8.1 - - - +
99A GLN* 2.7 36.6 - - - +
102A ILE* 4.1 21.5 - - + -
605A VAL* 4.5 7.0 - - + -
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Residues in contact with LYS 91 (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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87A TYR* 3.1 53.3 + - + +
90A VAL* 1.3 77.6 - - - +
92A GLY* 1.3 63.0 + - - +
94A ASP* 3.2 12.9 + - - +
95A TRP* 3.8 17.6 - - + +
608A THR* 5.5 0.4 - - + -
609A VAL 3.8 8.4 + - - +
610A ARG* 3.5 27.1 - - + +
611A ALA* 3.3 44.8 + - - +
612A TYR* 3.7 29.2 - - + +
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Residues in contact with GLY 92 (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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88A ASP 3.2 12.4 + - - -
89A THR* 2.9 10.7 + - - -
91A LYS* 1.3 80.9 - - - +
93A SER* 1.4 57.6 + - - +
94A ASP* 4.9 0.9 - - - +
146A GLY* 6.0 0.9 - - - -
302A CYS* 5.4 6.6 - - - +
304A ASP* 5.2 0.7 - - - +
415A ASN* 2.9 34.5 + - - +
417A LEU* 5.7 8.5 - - - -
610A ARG* 5.0 4.6 + - - -
612A TYR* 4.8 9.0 - - - -
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Residues in contact with SER 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 2.8 14.1 + - - -
90A VAL* 2.9 12.6 + - - +
92A GLY* 1.4 74.2 - - - +
94A ASP* 1.3 59.4 + - - +
95A TRP 3.9 1.1 - - - -
96A LEU* 3.4 1.7 - - - +
97A GLY* 3.5 24.2 + - - -
102A ILE* 4.9 0.5 - - - +
411A VAL 3.4 10.6 + - - -
412A HIS* 2.6 35.0 + - - -
413A GLY* 3.8 0.8 + - - -
414A ALA* 2.7 32.9 + - - +
415A ASN 3.8 1.9 + - - +
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Residues in contact with ASP 94 (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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90A VAL 2.9 3.2 + - - -
91A LYS 3.2 11.8 + - - -
93A SER* 1.3 78.0 - - - +
95A TRP* 1.4 69.6 + - - +
96A LEU 3.0 9.4 + - - -
414A ALA* 4.3 0.4 - - + -
554A ARG* 2.7 47.5 + - + +
565A ARG* 2.7 36.6 + - - -
610A ARG* 2.7 43.5 + - - +
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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