Contacts of the helix formed by residues 72 - 89 (chain I) in PDB entry 1SXG
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 72 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69I ASP* 2.8 28.8 + - + +
71I SER* 1.3 77.0 - - - +
73I ILE* 1.3 86.3 + - - +
74I PHE* 2.9 22.1 + - - +
75I TYR* 3.0 35.0 + - + -
76I ALA* 3.2 22.5 + - - +
221I TYR* 5.8 8.9 + - + +
247I THR* 6.0 2.6 - - - +
249I GLU* 3.8 15.5 + - - +
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Residues in contact with ILE 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ILE* 3.8 20.2 - - + +
278B ARG* 3.4 19.5 - - - +
279B LEU* 5.9 0.9 - - + -
282B MET* 6.0 0.2 - - + -
71I SER 4.1 2.0 - - - +
72I ASN* 1.3 76.3 - - - +
74I PHE* 1.3 55.8 + - - +
76I ALA* 3.3 6.5 + - + +
77I GLU* 2.8 35.7 + - + +
249I GLU* 3.4 17.2 + - + +
277I THR* 4.3 11.4 - - + -
278I ARG* 3.8 43.1 - - + +
279I LEU* 3.8 31.0 - - + -
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Residues in contact with PHE 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ASN* 2.9 17.7 - - - +
73I ILE* 1.3 76.8 - - - +
75I TYR* 1.3 80.9 + + - +
77I GLU* 3.2 3.2 + - - +
78I LEU* 2.7 53.8 + - + +
146I ALA* 3.9 17.3 - - + -
275I ASP* 3.3 35.2 - - + +
277I THR* 4.3 9.2 - - + +
292I GLN* 3.6 38.8 - - + -
294I MET* 3.5 32.1 - - + -
297I ILE* 5.6 0.4 - - + -
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Residues in contact with TYR 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67I ILE* 4.0 18.9 - - + +
68I PRO* 3.2 36.6 - - + -
69I ASP* 4.2 11.4 - - + +
72I ASN* 3.0 36.8 + - + +
74I PHE* 1.3 98.1 - + - +
76I ALA* 1.3 57.3 + - - +
78I LEU* 4.3 3.4 - - - -
79I ALA* 2.8 30.0 + - - +
100I GLN* 6.3 0.4 - - + -
123I MET* 3.7 25.5 - - + +
124I SER 4.0 12.9 + - - -
125I GLY* 4.2 10.6 + - - -
146I ALA* 5.1 8.9 + - + -
147I SER* 6.1 0.7 - - - -
189I GLU* 5.3 1.7 + - - -
221I TYR* 5.9 3.1 - - - -
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Residues in contact with ALA 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 3.9 33.8 - - + +
71B SER* 3.8 7.1 + - - +
76B ALA* 5.5 0.7 - - + -
67I ILE* 5.8 0.7 - - - -
69I ASP 5.3 0.2 + - - -
70I ILE* 4.1 15.4 + - - +
72I ASN 3.2 17.0 + - - +
73I ILE* 3.7 7.2 - - + +
75I TYR* 1.3 73.4 - - - +
77I GLU* 1.3 58.0 + - - +
79I ALA* 3.2 6.9 + - - +
80I ARG* 2.7 35.9 + - - +
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Residues in contact with GLU 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.8 13.5 + - - +
73I ILE* 2.8 19.9 + - + +
74I PHE* 3.6 3.8 - - - +
76I ALA* 1.3 77.8 - - - +
78I LEU* 1.3 65.7 + - - +
80I ARG* 3.2 5.2 - - + +
81I GLY* 3.1 14.9 + - - -
277I THR* 3.1 15.7 - - - -
278I ARG* 2.8 59.2 + - - +
294I MET* 3.8 24.2 - - + +
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Residues in contact with LEU 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74I PHE* 2.7 31.9 + - + +
75I TYR* 3.7 6.5 - - + +
77I GLU* 1.3 72.6 - - - +
79I ALA* 1.3 65.5 + - - +
81I GLY* 2.7 15.1 + - - -
82I ILE* 3.0 31.0 + - + +
123I MET* 3.4 25.6 - - - -
145I ALA* 4.1 3.1 - - + +
146I ALA* 3.6 29.4 - - + -
294I MET* 3.8 41.0 - - + +
297I ILE* 4.6 7.6 - - + -
298I GLY 4.5 3.8 - - - +
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Residues in contact with ALA 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.7 2.0 - - + -
65I VAL* 5.0 3.6 - - + -
67I ILE* 4.0 8.1 - - + -
75I TYR 2.8 23.0 + - - +
76I ALA* 3.5 6.1 - - - +
78I LEU* 1.3 71.2 - - - +
80I ARG* 1.3 63.6 + - - +
82I ILE* 2.8 25.2 + - - +
83I GLU* 3.0 17.5 + - - +
93I ILE* 4.9 1.2 - - - +
95I LEU* 3.5 35.3 - - + +
123I MET* 4.2 3.3 - - - +
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Residues in contact with ARG 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B PRO 3.5 3.6 + - - -
69B ASP* 3.6 23.8 + - - -
70B ILE* 4.0 11.2 - - + +
71B SER* 3.6 15.0 - - - +
97B ASN* 3.0 31.1 - - - +
99B ASP* 2.7 47.9 + - - +
76I ALA 2.7 16.8 + - - +
77I GLU* 3.2 12.6 - - + +
78I LEU 3.0 0.2 + - - -
79I ALA* 1.3 73.7 - - - +
81I GLY* 1.3 58.7 + - - +
83I GLU* 2.8 37.6 + - - +
84I ASP* 2.8 32.4 + - - +
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Residues in contact with GLY 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77I GLU 3.1 5.0 + - - -
78I LEU* 2.7 13.6 + - - -
80I ARG* 1.3 78.0 - - - +
82I ILE* 1.3 58.5 + - - -
84I ASP* 3.2 9.6 + - - +
85I ILE* 3.0 32.1 + - - +
294I MET* 5.6 3.1 - - - -
295I TYR* 4.7 15.4 - - - -
298I GLY* 5.5 2.0 - - - -
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Residues in contact with ILE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 5.8 0.9 - - + -
65I VAL* 4.8 16.6 - - + -
78I LEU* 3.0 24.8 + - + +
79I ALA* 2.8 17.5 + - - +
81I GLY* 1.3 76.6 - - - +
83I GLU* 1.3 56.1 + - - +
85I ILE* 3.2 10.6 + - - +
86I ALA* 2.9 24.4 + - - +
93I ILE* 3.5 19.3 - - + -
121I ILE* 4.2 31.2 - - + -
123I MET* 5.5 1.6 - - - -
145I ALA* 5.2 1.3 - - + -
298I GLY* 3.4 30.1 - - - +
301I ALA* 5.1 0.9 - - + -
302I MET* 4.7 14.6 - - + +
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Residues in contact with GLU 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ILE* 4.8 0.7 - - - +
97B ASN* 2.8 31.3 - - - +
104B LYS* 6.1 4.2 - - - -
79I ALA 3.0 7.1 + - - +
80I ARG* 2.8 59.3 + - - +
82I ILE* 1.3 73.1 - - - +
84I ASP* 1.3 66.9 + - - +
86I ALA* 3.4 4.3 - - - +
87I THR* 3.1 28.8 + - + +
93I ILE* 3.5 30.0 - - + +
95I LEU* 3.6 16.6 - - - +
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Residues in contact with ASP 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 5.4 4.1 - - - +
80I ARG* 2.8 34.5 + - - +
81I GLY* 3.2 11.8 + - - +
82I ILE 3.2 0.4 - - - -
83I GLU* 1.3 77.8 - - - +
85I ILE* 1.3 68.3 + - - +
87I THR* 3.0 23.1 + - - -
88I MET* 3.4 6.1 + - - +
295I TYR* 4.9 11.7 - - + -
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Residues in contact with ILE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I GLY 3.0 17.4 + - - +
82I ILE* 3.3 9.9 - - - +
84I ASP* 1.3 77.1 - - - +
86I ALA* 1.3 58.1 + - - +
88I MET* 2.8 30.5 + - - +
89I TYR* 3.1 40.9 + - + -
295I TYR* 3.2 48.0 - - + +
298I GLY* 4.1 2.0 - - - -
299I ALA* 3.9 31.0 - - + +
302I MET* 3.6 20.9 - - + -
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Residues in contact with ALA 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63I VAL* 5.2 0.9 - - + -
82I ILE 2.9 14.3 + - - +
83I GLU* 3.4 16.8 - - - +
85I ILE* 1.3 76.8 - - - +
87I THR* 1.3 57.4 + - + +
89I TYR* 3.1 7.8 + - - -
90I LYS 2.7 8.1 + - - -
91I TYR* 2.7 54.6 + - + +
93I ILE* 4.2 14.8 - - + -
302I MET* 4.6 7.3 - - - -
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Residues in contact with THR 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 4.3 24.0 - - - +
83I GLU* 3.1 16.5 + - + +
84I ASP* 3.0 16.9 + - - +
85I ILE 3.2 0.2 - - - -
86I ALA* 1.3 73.1 - - + +
88I MET* 1.3 64.9 + - - +
89I TYR 3.0 1.8 - - - -
90I LYS* 3.1 15.1 + - - +
91I TYR 4.7 4.3 - - - +
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Residues in contact with MET 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84I ASP 3.4 6.3 + - - +
85I ILE* 2.8 15.8 + - - +
87I THR* 1.3 82.6 + - - +
89I TYR* 1.3 73.6 + - + +
90I LYS* 3.4 0.6 + - - +
295I TYR* 4.6 15.9 - - - +
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Residues in contact with TYR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85I ILE* 3.1 44.4 + - + -
86I ALA 3.1 3.7 + - - +
87I THR 3.0 0.4 - - - -
88I MET* 1.3 93.1 - - + +
90I LYS* 1.3 82.8 + - - +
91I TYR* 3.2 43.3 + + + -
299I ALA* 4.1 3.2 + - - -
302I MET* 4.2 7.2 - - + -
303I ARG* 3.6 28.3 + - - +
306I THR* 3.6 20.2 - - + -
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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