Contacts of the helix formed by residues 84 - 97 (chain C) 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 GLU 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83C TYR* 1.3 69.7 - - - +
85C PRO* 1.3 76.5 - - + +
87C LEU* 3.0 7.4 + - + -
88C GLU* 2.8 35.4 + - + +
1031C EDO 4.6 11.5 - - - -
2D ASN* 3.6 27.8 + - - +
7D LEU* 3.8 24.2 - - + -
10D ARG* 3.9 15.5 + - - +
26D PHE* 3.6 5.2 - - - +
27D ALA 4.7 1.4 + - - -
38D VAL* 4.2 15.6 - - + +
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Residues in contact with PRO 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C GLN* 4.2 4.3 - - - +
83C TYR* 3.6 11.4 - - + -
84C GLU* 1.3 93.4 - - + +
86C TYR* 1.3 61.4 + - - +
88C GLU* 3.6 1.3 + - + +
89C LEU* 3.2 24.4 + - - +
302C PRO* 4.3 4.0 - - + +
305C CYS* 3.7 22.5 - - + +
306C VAL* 3.7 25.6 - - + +
309C LEU* 3.8 16.7 - - + +
1031C EDO 3.6 32.1 - - - +
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Residues in contact with TYR 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PHE* 3.3 52.7 - + + -
83C TYR* 3.5 19.4 + - + +
84C GLU 3.1 0.4 - - - -
85C PRO* 1.3 81.0 - - - +
87C LEU* 1.3 63.0 + - - +
89C LEU 3.4 0.2 + - - -
90C CYS* 3.3 40.8 + - - -
106C LEU* 4.1 10.6 - - - +
107C LEU* 3.1 44.3 + - + +
299C ALA* 3.9 11.5 - - + +
300C GLY* 3.6 21.1 - - - -
305C CYS* 3.6 12.0 - - - -
15D ILE* 3.6 15.7 - - + -
19D VAL* 4.5 8.3 - - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C PHE* 5.0 0.7 - - + -
83C TYR 3.5 8.3 + - - +
84C GLU* 3.0 8.7 + - + +
86C TYR* 1.3 78.2 - - - +
88C GLU* 1.3 63.7 + - - +
90C CYS* 3.3 3.6 + - - +
91C GLU* 3.1 33.5 + - + +
7D LEU* 3.6 44.9 - - + +
10D ARG* 3.7 23.1 - - + +
11D ARG* 3.6 29.6 - - - +
14D ALA* 4.5 2.5 - - + -
15D ILE* 4.2 18.2 - - + -
26D PHE* 3.9 14.8 - - + -
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C GLU* 2.8 28.9 + - + +
85C PRO* 4.1 3.7 - - - +
87C LEU* 1.3 73.5 - - - +
89C LEU* 1.3 65.7 + - - +
91C GLU* 3.2 17.5 + - + +
92C ILE* 3.0 37.5 + - + +
309C LEU* 4.1 23.7 - - + +
313C LYS* 5.0 10.6 + - - -
10D ARG* 4.6 7.9 - - - +
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C PRO 3.2 18.0 + - - +
86C TYR 3.9 4.0 - - - +
87C LEU 3.4 0.2 - - - -
88C GLU* 1.3 75.9 - - - +
90C CYS* 1.3 58.7 + - - +
92C ILE* 3.2 2.2 + - + +
93C MET* 2.9 48.0 + - + +
107C LEU* 4.0 21.3 - - + -
266C PHE* 5.0 2.9 - - + -
270C ILE* 5.2 1.8 - - + -
276C LEU* 3.7 31.0 - - + -
305C CYS* 4.6 7.2 - - - -
308C ALA* 3.7 18.4 - - + -
309C LEU* 3.7 18.8 - - + +
312C LEU* 3.8 28.7 - - + -
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Residues in contact with CYS 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 3.3 38.6 + - - -
87C LEU 3.6 7.9 - - - +
88C GLU 3.2 0.2 - - - -
89C LEU* 1.3 80.4 - - - +
91C GLU* 1.3 56.9 + - - +
94C ASN* 2.9 37.6 + - - +
105C THR* 3.5 47.0 + - - -
107C LEU* 3.7 8.1 - - - -
14D ALA* 4.1 4.3 - - + +
15D ILE* 3.9 15.0 - - + -
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Residues in contact with GLU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU* 3.1 17.5 + - + +
88C GLU* 3.5 13.8 - - - +
89C LEU 3.2 0.2 - - - -
90C CYS* 1.3 75.9 - - - +
92C ILE* 1.3 63.0 + - + +
94C ASN* 3.4 17.8 + - - +
95C GLN* 3.5 16.3 + - - +
10D ARG* 2.6 61.3 + - - +
14D ALA* 3.6 16.2 - - + -
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Residues in contact with ILE 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLU* 3.0 23.5 + - + +
89C LEU* 3.2 7.8 + - - +
91C GLU* 1.3 79.3 - - + +
93C MET* 1.3 57.6 + - - +
95C GLN* 3.0 9.9 + - + +
96C LYS* 2.8 54.6 + - + +
309C LEU* 3.6 28.9 - - + +
312C LEU* 3.7 24.0 - - + -
313C LYS* 6.3 2.9 - - - -
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Residues in contact with MET 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LEU* 2.9 28.4 + - + +
90C CYS* 4.0 1.1 - - - +
92C ILE* 1.3 73.4 - - - +
94C ASN* 1.3 66.5 + - - +
96C LYS* 4.2 9.2 - - + +
97C VAL* 2.9 30.9 + - + +
105C THR* 3.9 5.8 - - + +
251C LEU* 5.1 1.8 - - + -
252C PHE* 3.3 40.6 - - + -
266C PHE* 3.8 29.4 - - + -
270C ILE* 4.0 20.9 - - + -
280C THR* 3.6 17.4 - - - +
312C LEU* 4.0 25.6 - - - -
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Residues in contact with ASN 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C CYS 2.9 23.0 + - - +
91C GLU* 3.6 7.7 - - - +
92C ILE 3.2 0.2 - - - -
93C MET* 1.3 76.6 - - - +
95C GLN* 1.3 65.3 + - - +
101C PHE 5.1 0.2 - - - +
103C LYS* 2.8 57.5 + - + +
104C LYS* 3.0 18.7 + - - +
105C THR* 2.9 18.0 + - - -
280C THR* 4.3 0.9 - - - -
13D GLN 4.7 0.2 + - - -
14D ALA* 3.0 41.4 + - - +
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Residues in contact with GLN 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C GLU 3.7 12.0 + - - +
92C ILE* 3.0 9.9 + - + +
94C ASN* 1.3 89.3 + - - +
96C LYS* 1.3 66.4 + - + +
97C VAL 3.6 6.8 + - - +
103C LYS* 4.4 2.4 + - - +
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Residues in contact with LYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ILE* 2.8 44.0 + - + +
93C MET* 3.4 12.3 + - - -
95C GLN* 1.3 74.2 - - + +
97C VAL* 1.3 64.8 + - - +
98C PRO* 3.4 6.6 - - - +
251C LEU* 3.7 29.6 - - + +
252C PHE* 4.1 4.7 - - + -
255C GLU* 3.8 13.3 - - - +
312C LEU* 5.0 15.3 + - + -
316C GLU* 5.4 9.5 + - - +
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Residues in contact with VAL 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C MET* 2.9 26.2 + - + +
95C GLN 3.7 3.1 - - - +
96C LYS* 1.3 76.4 - - - +
98C PRO* 1.3 85.1 - - + +
99C GLY 3.5 0.2 + - - -
103C LYS* 2.9 25.1 + - + -
252C PHE* 3.9 24.0 - - + -
261C PRO* 5.2 0.7 - - + -
264C THR* 3.6 31.6 - - + +
266C PHE* 4.9 0.9 - - + -
280C THR* 3.5 34.5 - - + +
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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