Contacts of the helix formed by residues 75 - 90 (chain X) in PDB entry 3SDI
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 SER 75 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105P GLU* 2.6 29.5 + - - -
73X GLU 3.7 1.6 + - - -
74X LEU* 1.3 75.6 - - - +
76X PRO* 1.4 63.4 - - - +
77X GLN* 3.8 7.3 + - - +
78X ALA* 2.9 15.5 + - - +
79X VAL* 2.8 32.8 + - - +
105X ASP* 4.1 21.3 - - - -
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Residues in contact with PRO 76 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X HIS* 6.3 0.2 - - + -
41X THR* 3.9 17.0 - - + +
74X LEU 4.1 3.6 - - - +
75X SER* 1.4 83.2 - - - +
77X GLN* 1.3 56.9 + - - +
79X VAL* 3.3 5.8 + - + +
80X SER* 2.9 32.6 + - - -
101X ILE* 4.8 3.1 - - + +
103X GLY* 3.8 38.6 - - - +
104X TYR 4.1 2.9 - - - +
105X ASP* 4.0 22.9 - - + +
109X GLU* 3.4 17.7 - - + +
111X TYR* 3.9 11.9 - - + -
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Residues in contact with GLN 77 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P TYR 3.2 19.8 + - - -
104P ASN* 3.7 20.3 + - - +
105P GLU* 4.5 7.3 + - - +
75X SER* 3.2 8.9 - - - +
76X PRO* 1.3 79.4 - - - +
78X ALA* 1.3 58.1 + - - +
80X SER* 3.0 17.4 + - - -
81X SER* 3.0 24.9 + - - -
105X ASP* 5.8 4.9 - - - +
109X GLU* 3.6 10.0 + - - +
111X TYR* 3.3 24.6 - - + +
119X LYS* 3.4 12.2 + - - -
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Residues in contact with ALA 78 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103P TYR* 3.5 25.5 - - + +
105P GLU* 3.7 20.0 - - - +
74X LEU* 3.8 23.1 - - + -
75X SER* 2.9 21.2 + - - +
77X GLN* 1.3 77.5 - - - +
79X VAL* 1.3 64.6 + - - +
81X SER* 3.3 2.4 + - - -
82X PHE* 3.0 23.0 + - - +
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Residues in contact with VAL 79 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37X LEU* 3.7 30.5 - - + -
38X SER* 5.3 1.1 - - - +
41X THR* 4.1 18.4 - - + +
63X ILE* 4.1 28.3 - - + -
74X LEU* 3.9 24.4 - - + +
75X SER 2.8 21.7 + - - +
76X PRO* 3.6 7.9 - - + +
78X ALA* 1.3 71.2 - - - +
80X SER* 1.3 63.2 + - - +
82X PHE* 3.2 8.5 + - - +
83X VAL* 3.0 26.7 + - + +
101X ILE* 4.7 4.7 - - + -
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Residues in contact with SER 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76X PRO 2.9 15.0 + - - -
77X GLN 3.0 8.5 + - - -
79X VAL* 1.3 74.2 - - - +
81X SER* 1.3 59.6 + - - +
83X VAL* 3.1 2.8 + - - +
84X ARG* 2.9 28.9 + - - +
101X ILE* 3.8 21.1 - - - +
111X TYR* 3.7 28.8 - - - -
113X ILE* 3.8 3.6 - - - +
119X LYS* 2.9 30.2 + - - +
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Residues in contact with SER 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LYS 5.0 1.1 - - - +
102P THR 3.2 19.7 - - - +
103P TYR 3.7 14.4 - - - -
104P ASN* 3.3 24.3 + - - +
57W GLU* 5.7 0.4 - - - -
77X GLN* 3.0 27.1 + - - -
78X ALA 3.3 1.1 + - - -
80X SER* 1.3 81.2 + - - +
82X PHE* 1.3 63.0 + - - +
84X ARG* 3.8 6.7 + - - +
85X GLN* 3.1 21.7 + - - +
119X LYS* 3.4 9.8 + - - +
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Residues in contact with PHE 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102P THR* 3.3 27.0 + - + -
103P TYR* 3.9 24.2 - + + -
58X TYR* 5.3 0.4 - - - -
59X ILE* 3.8 26.7 - - + -
62X ASN* 3.5 42.2 - - + -
63X ILE* 4.0 19.5 - - + -
78X ALA 3.0 13.0 + - - +
79X VAL* 3.3 12.1 - - - +
80X SER 3.2 0.2 - - - -
81X SER* 1.3 78.1 - - - +
83X VAL* 1.3 65.5 + - + +
85X GLN* 3.5 4.7 + - - +
86X GLU* 3.1 49.6 + - + +
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Residues in contact with VAL 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X MET* 4.4 2.9 - - - -
55X PHE* 4.0 13.2 - - + -
59X ILE* 3.8 31.6 - - + -
79X VAL* 3.0 17.3 + - + +
80X SER 3.1 6.7 + - - +
82X PHE* 1.3 76.4 - - + +
84X ARG* 1.3 66.1 + - - +
86X GLU* 3.2 7.3 + - - +
87X LEU* 2.9 40.3 + - + +
99X VAL* 4.0 19.7 - - + -
101X ILE* 3.8 17.3 - - + -
113X ILE* 4.1 4.3 - - + -
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Residues in contact with ARG 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W THR* 3.2 25.3 + - - +
53W THR* 3.3 26.9 - - - +
54W THR* 2.6 33.7 + - - +
57W GLU* 3.5 21.9 + - - -
80X SER 2.9 16.5 + - - +
81X SER* 3.8 9.1 + - - +
83X VAL* 1.3 76.2 - - - +
85X GLN* 1.3 64.5 + - - +
87X LEU* 3.0 4.9 + - - +
88X ALA* 2.8 38.7 + - - +
113X ILE* 4.3 11.1 - - + +
117X GLY* 2.7 47.8 + - - +
119X LYS* 3.7 33.0 - - + +
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Residues in contact with GLN 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P LYS* 3.1 50.3 + - - +
102P THR* 3.1 34.8 + - - +
57W GLU* 5.5 4.2 + - - +
81X SER 3.1 15.4 + - - +
82X PHE* 3.9 6.2 - - - +
84X ARG* 1.3 85.4 - - - +
86X GLU* 1.3 66.5 + - - +
88X ALA* 3.4 7.7 + - + +
89X LYS* 3.0 48.2 + - + +
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Residues in contact with GLU 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X PHE* 4.4 9.5 - - + -
58X TYR* 2.9 35.4 + - + -
59X ILE* 4.2 13.7 - - + -
82X PHE* 3.1 45.4 + - + +
83X VAL 3.2 9.2 + - - +
85X GLN* 1.3 81.5 - - + +
87X LEU* 1.3 61.9 + - - +
89X LYS* 3.3 30.9 + - - +
90X SER* 3.2 20.4 + - - -
95X TYR* 5.4 1.8 - - + -
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Residues in contact with LEU 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X PHE* 3.5 33.4 - - + -
83X VAL* 2.9 24.6 + - + +
84X ARG 3.6 5.4 - - - +
86X GLU* 1.3 75.5 - - - +
88X ALA* 1.3 56.8 + - - +
90X SER* 2.9 38.0 + - - +
95X TYR* 4.5 17.7 - - + -
97X VAL* 4.1 16.6 - - + +
99X VAL* 4.5 5.2 - - + -
113X ILE* 3.7 20.6 - - + -
114X ASP 3.7 18.4 - - - +
115X TYR* 3.9 15.6 - - - +
117X GLY* 3.9 11.9 - - - -
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Residues in contact with ALA 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50W THR* 3.9 18.2 - - - +
54W THR* 4.0 17.9 - - + +
84X ARG* 2.8 28.9 + - - +
85X GLN* 3.8 6.5 - - + +
87X LEU* 1.3 72.0 - - - +
89X LYS* 1.3 60.9 + - - +
90X ILE* 3.5 22.0 + - + +
116X LEU 3.9 10.1 - - - +
117X GLY* 4.1 1.0 - - - -
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Residues in contact with LYS 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101P LYS* 5.7 3.1 - - - +
85X GLN* 3.0 40.5 + - + +
86X GLU* 3.5 29.7 + - - +
87X LEU 3.2 0.2 - - - -
88X ALA* 1.3 76.0 - - - +
90X SER* 1.3 77.3 + - - +
91X SER* 3.6 10.1 + - - -
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Residues in contact with SER 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86X GLU 3.2 9.3 + - - -
87X LEU* 3.0 11.6 + - - +
89X LYS* 1.3 75.3 - - - +
90X ILE* 1.3 70.0 + - - +
91X SER* 3.0 25.2 + - - -
93X ARG 5.4 0.4 - - - -
94X PRO* 3.2 13.1 - - - +
95X TYR* 3.0 52.5 + - - +
115X TYR 4.8 1.9 + - - -
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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
------------------------------------------------------------
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