Contacts of the helix formed by residues 75 - 90 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 3.1 26.6 + - - -
72J TYR* 5.8 0.8 - - - -
73J GLU 3.6 2.7 + - - -
74J LEU* 1.3 76.5 - - - +
76J PRO* 1.4 73.2 - - - +
77J GLN* 3.5 7.9 + - - +
78J ALA* 3.0 25.9 + - - +
79J VAL* 3.0 12.2 + - - +
105J ASP* 4.2 15.7 - - - -
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Residues in contact with PRO 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J THR* 4.0 16.4 - - + +
74J LEU 3.8 1.5 - - - +
75J SER* 1.4 86.7 - - - +
77J GLN* 1.3 62.1 + - - +
79J VAL* 3.2 4.6 + - + +
80J SER* 2.9 26.3 + - - -
101J ILE* 4.9 3.7 - - + +
102J GLY 5.5 0.2 - - - -
103J GLY* 3.9 27.8 - - - +
104J TYR 4.0 3.1 - - - +
105J ASP* 3.8 41.3 - - + +
109J GLU* 3.9 13.5 - - + +
111J TYR* 3.9 12.2 - - + -
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Residues in contact with GLN 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR 3.1 20.8 + - - -
104B ASN* 3.5 21.8 + - - +
105B GLU* 4.3 6.9 + - - +
75J SER* 3.2 9.1 + - - +
76J PRO* 1.3 80.0 - - - +
78J ALA* 1.3 58.0 + - - +
80J SER* 3.1 4.9 + - - -
81J SER* 3.0 36.2 + - - -
105J ASP* 5.9 4.7 - - - +
109J GLU* 3.9 4.8 + - - +
111J TYR* 3.5 24.1 + - + +
119J LYS* 3.4 10.4 + - - +
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Residues in contact with ALA 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B TYR* 3.5 29.5 - - + +
105B GLU* 3.8 17.5 - - - +
74J LEU* 3.9 22.0 - - + -
75J SER* 3.0 22.2 + - - +
77J GLN* 1.3 77.1 - - - +
79J VAL* 1.3 60.0 + - - +
81J SER* 3.4 1.4 + - - -
82J PHE* 3.0 28.2 + - - +
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Residues in contact with VAL 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37J LEU* 3.7 31.0 - - + -
38J SER* 5.4 1.1 - - - +
41J THR* 4.1 19.1 - - + +
63J ILE* 4.2 28.9 - - + -
74J LEU* 3.9 24.9 - - + +
75J SER 3.0 14.5 + - - +
76J PRO 3.8 6.3 - - - +
78J ALA* 1.3 74.8 - - - +
80J SER* 1.3 59.1 + - - +
82J PHE* 3.3 7.4 + - - +
83J VAL* 2.9 30.1 + - + +
101J ILE* 4.6 6.3 - - + -
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Residues in contact with SER 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J PRO 2.9 14.6 + - - -
77J GLN 3.1 7.3 + - - -
79J VAL* 1.3 75.8 - - - +
81J SER* 1.3 57.8 + - - +
83J VAL* 3.2 2.6 + - - +
84J ARG* 2.9 29.8 + - - +
101J ILE* 3.7 19.5 - - - -
111J TYR* 3.7 29.4 - - - -
113J ILE* 3.8 4.5 - - - +
119J LYS* 2.8 33.8 + - - +
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Residues in contact with SER 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS 5.3 1.4 - - - +
102B THR 3.2 16.9 - - - +
103B TYR 3.7 15.3 - - - -
104B ASN* 3.4 17.9 + - - +
57I GLU* 5.6 1.3 - - - -
77J GLN* 3.0 31.5 + - - -
78J ALA 3.8 0.7 - - - -
79J VAL 3.4 0.2 - - - -
80J SER* 1.3 78.2 + - - +
82J PHE* 1.3 62.6 + - - +
84J ARG* 3.4 8.2 + - - +
85J GLN* 3.1 21.7 + - - +
119J LYS* 3.5 8.6 + - - +
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Residues in contact with PHE 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 3.2 30.2 + - + -
103B TYR* 4.0 24.2 - + + -
58J TYR* 5.2 0.9 - + - -
59J ILE* 3.9 23.1 - - + -
62J ASN* 3.8 39.3 - - + -
63J ILE* 3.7 22.4 - - + -
78J ALA 3.0 17.7 + - - +
79J VAL* 3.5 7.4 - - - +
80J SER 3.2 0.2 - - - -
81J SER* 1.3 79.3 - - - +
83J VAL* 1.3 66.5 + - + +
85J GLN* 3.4 5.0 + - - +
86J GLU* 3.2 43.4 + - + +
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Residues in contact with VAL 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43J MET* 4.4 3.4 - - - -
55J PHE* 4.1 11.0 - - + -
59J ILE* 3.6 38.1 - - + -
79J VAL* 2.9 23.0 + - + +
80J SER 3.7 3.1 - - - +
82J PHE* 1.3 76.9 - - + +
84J ARG* 1.3 66.9 + - - +
86J GLU* 3.1 4.7 + - - +
87J LEU* 3.0 38.1 + - + +
99J VAL* 4.0 13.0 - - + -
101J ILE* 3.9 16.8 - - + -
113J ILE* 4.0 12.3 - - + -
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Residues in contact with ARG 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I THR* 3.3 24.4 + - - -
53I THR* 3.3 23.8 - - - +
54I THR* 3.0 27.7 + - - +
57I GLU* 2.9 29.1 + - - -
80J SER 2.9 16.6 + - - +
81J SER* 3.7 8.4 + - - +
83J VAL* 1.3 75.7 - - - +
85J GLN* 1.3 65.4 + - - +
87J LEU* 3.0 4.9 + - - +
88J ALA* 2.8 37.6 + - - +
113J ILE* 4.3 12.9 - - + +
117J GLY 2.9 40.9 + - - +
119J LYS* 3.7 29.8 - - + +
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Residues in contact with GLN 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 2.9 53.9 + - - +
102B THR* 3.0 33.1 + - - +
57I GLU* 5.4 2.7 + - - +
81J SER 3.1 13.8 + - - +
82J PHE* 3.6 7.8 - - - +
84J ARG* 1.3 87.5 - - - +
86J GLU* 1.3 65.2 + - + +
88J ALA* 3.3 7.0 + - + +
89J LYS* 3.0 47.2 + - + +
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Residues in contact with GLU 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J PHE* 4.2 17.9 - - + -
58J TYR* 3.1 32.2 + - - -
59J ILE* 4.2 11.0 - - + -
82J PHE* 3.2 36.3 + - + +
83J VAL 3.1 9.0 + - - +
85J GLN* 1.3 79.3 - - + +
87J LEU* 1.3 62.2 + - - +
89J LYS* 3.1 35.7 + - - +
90J SER* 3.2 21.5 + - - -
95J TYR* 5.2 3.9 - - + -
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Residues in contact with LEU 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55J PHE* 3.5 35.0 - - + -
83J VAL* 3.0 21.0 + - + +
84J ARG 3.0 8.0 + - - +
86J GLU* 1.3 74.8 - - - +
88J ALA* 1.3 65.5 + - - +
90J SER* 3.0 30.3 + - - +
95J TYR* 4.4 17.7 - - + +
97J VAL* 4.2 19.3 - - + +
99J VAL* 4.6 4.9 - - + -
113J ILE* 3.5 28.7 - - + -
114J ASP 3.6 8.1 - - - +
115J TYR* 4.0 13.7 - - - +
116J LEU 4.5 0.4 - - - -
117J GLY* 3.9 13.2 - - - +
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Residues in contact with ALA 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50I THR* 4.1 7.2 - - - +
54I THR* 4.2 10.8 - - - +
84J ARG* 2.8 41.2 + - - +
85J GLN* 3.7 7.6 - - + +
87J LEU* 1.3 73.3 - - - +
89J LYS* 1.3 60.3 + - - +
90J ILE* 3.3 23.2 + - - +
116J LEU 3.9 10.5 - - - +
117J GLY* 4.1 1.4 - - - -
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Residues in contact with LYS 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B LYS* 6.1 0.9 - - - +
85J GLN* 3.0 32.6 + - + +
86J GLU* 3.1 38.9 + - - +
88J ALA* 1.3 76.4 - - - +
90J SER* 1.3 78.2 + - - +
91J SER* 3.5 10.3 + - - -
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Residues in contact with SER 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86J GLU 3.2 10.4 + - - -
87J LEU* 3.0 10.0 + - - -
89J LYS* 1.3 82.2 - - - +
90J ILE* 1.3 59.5 + - - +
91J SER* 2.7 34.8 + - - -
93J ARG 5.3 0.4 - - - -
94J PRO* 3.3 10.2 - - - +
95J TYR* 2.9 54.0 + - - +
115J TYR 4.9 1.2 + - - -
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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