Contacts of the helix formed by residues 84 - 101 (chain C) in PDB entry 5LSW
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 ALA 84 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C THR* 1.3 74.5 - - - +
85C HIS* 1.3 56.9 + - - +
87C SER* 3.8 1.6 - - - -
88C ASN* 2.8 29.5 + - - +
130C ARG* 6.1 2.2 - - - -
131C PRO* 3.6 20.8 - - + +
792D GLY* 4.0 18.8 - - - -
793D ILE* 3.9 18.2 - - + +
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Residues in contact with HIS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 2.8 36.5 + - - -
83C THR* 3.2 7.2 + - - +
84C ALA* 1.3 77.6 - - - +
86C GLN* 1.3 64.7 + - - +
88C ASN* 3.5 3.9 - - - +
89C ARG* 3.1 33.1 + - + +
790D GLU 4.7 4.5 - - - +
791D GLY* 3.2 39.9 + - - +
792D GLY* 4.5 1.0 - - - -
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN 5.7 1.0 + - - -
73C ILE* 4.5 15.4 - - + +
76C SER* 3.3 22.1 + - - -
81C THR 3.9 3.8 - - - +
82C LEU* 3.5 23.3 - - + -
83C THR* 3.0 37.3 + - - +
85C HIS* 1.3 80.0 - - - +
87C SER* 1.3 64.2 + - - +
89C ARG* 3.5 4.1 + - - +
90C VAL* 3.1 27.5 + - - +
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Residues in contact with SER 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 3.9 11.3 - - - +
83C THR 2.9 16.9 + - - -
84C ALA 3.8 3.6 - - - -
86C GLN* 1.3 74.7 - - - +
88C ASN* 1.3 66.3 + - - +
90C VAL* 3.3 7.6 - - - +
91C CYS* 2.8 30.5 + - - +
131C PRO* 2.7 35.7 + - - -
134C TYR* 3.6 14.5 - - - -
135C LEU* 3.7 8.8 + - - +
793D ILE* 4.1 3.1 - - - -
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Residues in contact with ASN 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 5.7 1.4 + - - -
40C LEU* 5.8 2.8 - - - +
84C ALA 2.8 19.2 + - - +
85C HIS* 3.5 8.1 + - - +
86C GLN 3.3 0.2 - - - -
87C SER* 1.3 78.1 - - - +
89C ARG* 1.3 64.3 + - - +
91C CYS* 3.9 2.4 - - - +
92C ASN* 3.2 32.8 + - - +
134C TYR* 4.4 11.5 + - - -
791D GLY* 3.0 32.2 + - - +
792D GLY 3.5 14.5 + - - +
793D ILE* 4.7 0.9 - - + +
797D MET* 3.3 16.9 - - + +
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Residues in contact with ARG 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C PRO* 4.5 11.9 + - - +
35C ARG* 3.9 19.2 - - - +
36C GLU* 3.3 52.8 + - + +
39C LEU* 4.2 13.0 - - + +
69C GLU* 2.8 42.0 + - - +
72C ASN* 5.7 1.0 - - - +
85C HIS* 3.1 22.2 + - - +
86C GLN* 4.1 4.7 - - - +
88C ASN* 1.3 78.0 - - - +
90C VAL* 1.3 64.5 + - - +
92C ASN* 3.1 21.3 + - - +
93C ALA* 3.3 7.8 + - - +
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Residues in contact with VAL 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C GLU* 3.9 25.4 - - + +
70C ILE* 3.9 19.5 - - + -
73C ILE* 3.7 35.9 - - + -
86C GLN 3.1 21.3 + - - +
87C SER* 3.3 10.1 - - - +
89C ARG* 1.3 79.5 - - - +
91C CYS* 1.3 60.3 + - - +
93C ALA* 3.1 6.8 + - - +
94C LEU* 2.9 27.0 + - + +
122C PHE* 4.5 6.1 - - + -
135C LEU* 3.7 16.8 - - + -
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Residues in contact with CYS 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87C SER* 2.8 22.8 + - - +
88C ASN 3.9 1.6 - - - +
90C VAL* 1.3 74.1 - - - +
92C ASN* 1.3 61.3 + - - +
94C LEU* 3.7 7.7 - - - +
95C ALA* 3.0 26.7 + - - +
134C TYR* 3.5 32.8 - - + +
135C LEU* 3.7 25.6 - - - -
138C THR* 3.4 35.5 - - + +
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Residues in contact with ASN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C GLU* 5.1 1.6 + - - +
39C LEU* 4.0 21.8 - - + +
40C LEU* 3.8 29.5 - - - +
43C SER* 3.3 25.1 + - - +
88C ASN* 3.2 27.8 + - - +
89C ARG* 3.1 15.0 + - - +
91C CYS* 1.3 77.3 - - - +
93C ALA* 1.3 61.2 + - - +
95C ALA* 3.3 12.0 + - - +
96C LEU* 3.3 17.7 + - - +
134C TYR* 5.4 3.5 + - - -
797D MET* 6.1 0.2 - - - +
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Residues in contact with ALA 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 3.9 23.2 - - + +
66C LEU* 4.0 18.6 - - + +
69C GLU* 4.1 22.2 - - + -
70C ILE* 5.1 4.9 - - + -
89C ARG 3.3 5.8 + - - +
90C VAL* 3.1 9.5 + - - +
92C ASN* 1.3 78.5 - - - +
94C LEU* 1.3 64.1 + - - +
96C LEU* 3.1 14.0 + - - +
97C LEU* 3.1 17.9 + - - +
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Residues in contact with LEU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.6 33.0 - - + -
90C VAL* 2.9 20.2 + - + +
91C CYS* 3.7 7.4 - - - +
92C ASN 3.3 0.2 - - - -
93C ALA* 1.3 76.4 - - - +
95C ALA* 1.3 57.4 + - - +
97C LEU* 3.1 5.9 + - + +
98C GLN 2.9 24.6 + - - -
119C LEU* 3.8 26.2 - - + -
122C PHE* 4.2 5.2 - - + -
135C LEU* 3.7 23.3 - - + -
138C THR* 3.7 21.3 - - + -
139C SER* 3.7 22.7 - - - +
142C VAL* 3.5 13.2 - - + +
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Residues in contact with ALA 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C SER* 4.5 14.8 - - - +
46C ARG* 3.3 38.2 - - - +
91C CYS 3.0 17.5 + - - +
92C ASN* 3.6 7.4 - - - +
93C ALA 3.2 0.6 - - - -
94C LEU* 1.3 75.3 - - - +
96C LEU* 1.3 62.2 + - - +
98C GLN* 3.4 5.0 + - - +
99C CYS 3.2 15.9 + - - -
138C THR* 4.6 5.3 - - + +
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Residues in contact with LEU 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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29C LEU* 4.5 4.3 - - + -
39C LEU* 4.0 25.8 - - + +
42C LEU* 4.0 32.1 - - + +
43C SER* 4.0 27.6 - - - +
46C ARG* 5.1 3.4 - - + -
52C LEU* 4.1 17.0 - - + -
56C LEU* 4.0 11.2 - - + +
66C LEU* 4.0 19.3 - - + -
92C ASN 3.3 10.3 + - - +
93C ALA 3.1 8.8 + - - +
95C ALA* 1.3 78.1 - - - +
97C LEU* 1.3 65.7 + - - +
99C CYS* 3.4 6.8 + - - +
100C VAL* 3.2 25.3 + - - +
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Residues in contact with LEU 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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63C ILE* 5.1 9.4 - - + -
66C LEU* 3.9 29.2 - - + -
67C LEU* 4.3 7.6 - - + -
70C ILE* 3.4 33.4 - - + -
93C ALA 3.1 14.6 + - - +
94C LEU* 3.1 14.9 + - + +
96C LEU* 1.3 75.9 - - - +
98C GLN* 1.3 59.9 + - - +
100C VAL* 3.1 6.8 + - + +
101C ALA* 2.8 29.3 + - - +
110C PHE* 3.6 19.0 - - + -
115C ILE* 4.0 24.9 - - + -
119C LEU* 4.4 4.5 - - + -
142C VAL* 4.4 7.0 - - + -
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ARG* 3.4 24.2 + - - +
94C LEU 2.9 8.1 + - - +
95C ALA* 3.7 10.4 - - - +
96C LEU 3.3 0.2 - - - -
97C LEU* 1.3 75.0 - - - +
99C CYS* 1.3 61.1 + - - +
101C ALA* 3.2 3.9 + - - +
102C SER* 2.8 29.2 + - - +
138C THR* 4.9 2.8 - - - +
141C GLY* 3.7 21.9 - - - +
142C VAL* 3.7 24.1 + - + +
145C ALA* 3.6 19.3 - - + +
804D ASN* 3.3 33.7 + - - +
808D ILE* 4.0 9.0 - - - +
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Residues in contact with CYS 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ARG* 3.8 21.9 - - + +
49C VAL 5.7 0.4 - - - -
52C LEU* 4.0 22.2 - - - -
53C ALA* 3.4 42.5 - - - +
56C LEU* 4.4 2.0 - - - -
95C ALA 3.2 10.4 + - - +
96C LEU* 3.4 12.8 - - - +
97C LEU 3.2 0.2 - - - -
98C GLN* 1.3 80.3 - - - +
100C VAL* 1.3 60.5 + - - +
102C SER* 3.4 13.6 + - - -
103C HIS* 3.5 8.1 + - - +
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Residues in contact with VAL 100 (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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53C ALA* 3.7 26.9 - - + +
56C LEU* 4.1 13.2 - - + -
57C TRP* 3.5 28.0 - - + -
63C ILE* 4.6 11.0 - - + -
66C LEU* 6.0 0.4 - - + -
96C LEU 3.2 14.2 + - - +
97C LEU* 3.1 12.4 + - + +
99C CYS* 1.3 74.4 - - - +
101C ALA* 1.3 64.2 + - - +
102C SER 3.4 0.3 + - - -
103C HIS 3.7 2.1 + - - -
106C THR* 2.7 33.5 + - - +
107C ARG* 3.8 7.1 + - - -
110C PHE* 3.5 18.6 - - + -
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Residues in contact with ALA 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU 2.8 19.8 + - - +
98C GLN* 3.2 9.6 + - - +
100C VAL* 1.3 74.5 - - - +
102C SER* 1.3 57.4 + - - +
107C ARG* 3.2 28.8 + - - +
110C PHE* 3.7 33.0 - - + -
142C VAL* 4.3 8.1 - - + +
145C ALA 5.3 0.2 - - - -
146C LEU* 3.6 26.4 - - + +
149C THR* 4.6 0.2 - - - +
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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