Contacts of the helix formed by residues 83 - 97 (chain A) in PDB entry 1SZU
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 TYR 83 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 5.0 3.6 - - + -
76A THR* 3.1 31.9 - - + -
77A CYS* 4.3 3.5 + - - -
78A PHE* 3.6 33.5 + - + +
82A ALA* 1.3 78.6 - - - +
84A GLU* 1.3 65.3 + - - +
85A PRO* 4.1 10.5 - - + -
86A TYR* 3.5 32.5 + - + +
87A LEU 3.6 3.8 + - - -
299A ALA 3.3 11.3 + - - -
300A GLY 2.5 31.7 + - - -
301A ASN* 4.2 0.3 - - - -
302A PRO* 3.6 37.1 - - + +
305A CYS* 4.6 0.2 - - - -
1030A EDO 4.4 6.1 - - - -
26B PHE* 3.6 11.1 - - - -
27B ALA* 3.7 18.4 - - + +
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Residues in contact with GLU 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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83A TYR* 1.3 66.5 - - - +
85A PRO* 1.3 75.9 - - + +
86A TYR 3.1 2.5 - - - -
87A LEU* 3.0 7.5 + - + +
88A GLU* 2.8 29.7 + - + +
1030A EDO 4.7 9.4 - - - -
2B ASN* 4.8 8.9 + - - -
7B LEU* 3.9 39.4 - - + +
10B ARG* 4.3 8.5 + - - -
26B PHE* 4.4 3.1 - - + -
27B ALA 4.8 0.8 + - - -
28B ASP* 5.2 4.2 - - - +
38B VAL* 3.8 20.4 - - + +
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Residues in contact with PRO 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 4.3 3.1 - - - +
83A TYR* 3.6 10.1 - - + -
84A GLU* 1.3 93.5 - - + +
86A TYR* 1.3 61.8 + - - +
88A GLU* 3.6 3.0 + - + +
89A LEU* 3.2 24.8 + - - +
302A PRO* 4.3 3.1 - - + +
305A CYS* 3.6 25.0 - - + +
306A VAL* 3.7 23.8 - - + +
309A LEU* 4.0 14.4 - - + +
1030A EDO 3.5 36.6 - - - +
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Residues in contact with TYR 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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78A PHE* 3.5 52.3 - + + -
83A TYR* 3.5 18.9 + - + +
84A GLU 3.1 0.8 - - - -
85A PRO* 1.3 80.4 - - - +
87A LEU* 1.3 64.4 + - - +
89A LEU 3.4 0.2 + - - -
90A CYS* 3.2 40.7 + - - -
106A LEU* 4.0 11.1 - - - +
107A LEU* 3.1 51.1 + - + +
299A ALA* 3.8 12.8 - - + +
300A GLY 3.7 15.0 - - - -
305A CYS* 3.7 11.1 - - - -
15B ILE* 3.9 14.8 - - + +
19B VAL* 4.5 7.4 - - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 5.2 1.3 - - + -
83A TYR 3.6 1.8 + - - -
84A GLU* 3.0 9.0 + - + +
86A TYR* 1.3 82.8 - - - +
88A GLU* 1.3 64.9 + - - +
90A CYS* 3.1 4.5 + - - +
91A GLU* 3.0 33.1 + - - +
7B LEU* 3.8 26.5 - - + +
10B ARG* 3.5 61.7 - - + +
11B ARG* 3.6 9.9 - - + +
14B ALA* 4.1 9.4 - - + -
15B ILE* 4.2 10.1 - - + -
26B PHE* 4.0 18.2 - - + -
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Residues in contact with GLU 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 GLU* 2.8 23.2 + - + +
85A PRO* 3.9 5.1 - - - +
87A LEU* 1.3 73.5 - - - +
89A LEU* 1.3 63.6 + - - +
91A GLU* 3.1 19.6 + - - +
92A ILE* 3.0 36.5 + - + +
309A LEU* 3.9 29.1 - - + +
313A LYS* 5.0 8.3 + - - -
10B ARG* 4.7 7.4 - - - +
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Residues in contact with LEU 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 PRO 3.2 15.5 + - - +
86A TYR 3.8 3.8 - - - +
88A GLU* 1.3 78.5 - - - +
90A CYS* 1.3 58.4 + - - +
92A ILE* 3.3 1.8 + - + -
93A MET* 2.8 49.9 + - + +
107A LEU* 4.0 21.5 - - + -
266A PHE* 5.1 4.0 - - + -
270A ILE* 5.4 2.0 - - + -
276A LEU* 3.4 32.5 - - + -
305A CYS* 4.6 5.4 - - - +
308A ALA* 3.7 17.5 - - + -
309A LEU* 3.8 19.2 - - + +
312A LEU* 3.9 28.3 - - + -
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Residues in contact with CYS 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 TYR* 3.2 39.2 + - - -
87A LEU 3.1 9.0 + - - +
89A LEU* 1.3 79.1 - - - +
91A GLU* 1.3 63.0 + - - +
93A MET 3.2 0.7 + - - -
94A ASN* 2.9 30.5 + - - +
105A THR* 3.4 46.1 + - - -
107A LEU* 3.8 6.7 - - - -
14B ALA* 4.1 5.4 - - + +
15B ILE* 3.7 15.7 - - + -
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Residues in contact with GLU 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 LEU* 3.0 19.0 + - + +
88A GLU* 3.4 14.5 - - - +
90A CYS* 1.3 77.2 - - - +
92A ILE* 1.3 62.7 + - + +
94A ASN* 3.3 17.6 + - - +
95A GLN* 3.4 17.2 + - - +
10B ARG* 2.7 61.5 + - - +
14B ALA* 3.7 16.8 - - + +
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Residues in contact with ILE 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 GLU* 3.0 29.8 + - + +
89A LEU* 3.7 4.7 - - - +
91A GLU* 1.3 76.4 - - + +
93A MET* 1.3 59.9 + - - +
95A GLN* 3.1 7.3 + - - +
96A LYS* 2.9 45.6 + - + +
309A LEU* 3.7 27.6 - - + +
312A LEU* 3.5 29.4 - - + -
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Residues in contact with MET 93 (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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89A LEU* 2.8 42.2 + - + +
90A CYS 3.8 0.4 - - - +
92A ILE* 1.3 70.9 - - - +
94A ASN* 1.3 67.4 + - - +
96A LYS* 4.4 6.1 - - - +
97A VAL* 3.0 31.8 + - + +
105A THR* 3.7 8.5 - - + +
251A LEU* 5.5 0.9 - - + -
252A PHE* 3.5 37.0 - - + -
266A PHE* 3.7 32.1 - - + -
270A ILE* 3.8 26.2 - - + -
280A THR* 3.6 15.7 - - - +
312A LEU* 4.2 11.9 - - - -
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Residues in contact with ASN 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 CYS 2.9 18.2 + - - -
91A GLU* 3.5 9.7 - - - +
92A ILE 3.2 0.2 - - - -
93A MET* 1.3 76.1 - - - +
95A GLN* 1.3 64.5 + - - +
101A PHE 5.2 0.2 - - - +
103A LYS* 2.8 53.4 + - + +
104A LYS* 3.0 16.5 + - - +
105A THR* 2.8 22.0 + - - -
280A THR* 3.9 5.9 - - - +
13B GLN 4.7 0.2 + - - -
14B ALA* 3.1 37.6 + - - +
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Residues in contact with GLN 95 (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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91A GLU 3.4 12.9 + - - +
92A ILE* 3.1 8.9 + - - +
93A MET 3.1 0.6 - - - -
94A ASN* 1.3 83.0 + - - +
96A LYS* 1.3 66.4 + - + +
97A VAL 3.5 6.6 + - - +
103A LYS* 4.4 2.3 + - - +
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Residues in contact with LYS 96 (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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92A ILE* 2.9 38.8 + - + +
93A MET* 4.2 7.6 - - - +
95A GLN* 1.3 76.0 - - + +
97A VAL* 1.3 63.6 + - - +
98A PRO* 3.5 6.1 - - - +
251A LEU* 3.7 30.3 - - + +
252A PHE* 4.2 5.5 - - + -
255A GLU* 3.8 14.4 - - - +
312A LEU* 5.3 12.0 + - + -
316A GLU* 4.8 13.1 + - - +
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Residues in contact with VAL 97 (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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93A MET* 3.0 27.9 + - + +
95A GLN 3.7 3.1 - - - +
96A LYS* 1.3 75.7 - - - +
98A PRO* 1.3 86.0 - - + +
99A GLY 3.6 0.2 + - - -
103A LYS* 3.0 23.1 + - + -
252A PHE* 3.8 25.6 - - + -
261A PRO* 5.5 0.4 - - + -
264A THR* 3.6 30.7 - - + +
266A PHE* 5.0 0.4 - - + -
280A THR* 3.7 33.7 - - + +
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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