Contacts of the helix formed by residues 90 - 107 (chain B) in PDB entry 3SJ5
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 ARG 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ARG* 1.3 75.4 - - - +
91B LEU* 1.3 65.1 + - - +
92B VAL* 3.6 21.5 - - + +
93B ASN* 3.1 28.9 + - - +
94B PHE* 3.0 20.1 + - - +
152B PHE* 4.1 2.2 - - - -
154B GLU* 3.6 24.1 + - - +
180B ASN* 5.3 6.9 + - - +
181B PRO 3.6 20.2 + - - -
182B VAL* 3.0 24.4 + - - +
183B PHE 4.5 6.8 + - - -
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 1.3 71.6 - - - +
92B VAL* 1.3 62.7 + - - +
94B PHE* 3.2 6.5 + - + +
95B LEU* 2.9 38.5 + - + +
145B ILE 5.4 0.2 - - - +
148B SER* 3.7 36.6 - - - +
149B SER* 3.8 11.9 - - - -
152B PHE* 3.8 18.3 - - + -
154B GLU* 2.8 44.5 + - + +
156B ILE* 3.7 31.9 - - + -
178B PHE* 3.9 11.0 - - + -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ARG* 3.6 39.9 - - + +
91B LEU* 1.3 79.0 - - - +
93B ASN* 1.3 66.3 + - - +
95B LEU* 3.5 2.7 + - - +
96B MET* 3.0 40.2 + - + +
127B ILE* 3.8 31.0 - - + -
154B GLU* 4.8 1.6 + - - +
178B PHE* 3.9 25.6 - - + -
182B VAL* 4.0 21.8 - - + +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ARG* 5.2 4.4 - - + -
90B ARG* 3.1 41.0 + - - +
92B VAL* 1.3 81.8 - - - +
94B PHE* 1.3 65.7 - - - +
96B MET* 3.3 10.5 + - - +
97B MET* 3.1 36.6 + - + +
182B VAL 5.8 0.2 + - - -
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ILE* 4.8 1.1 - - + -
85B TYR 3.5 21.3 - - - -
86B PHE* 3.5 38.4 - + - -
89B ARG* 5.0 5.3 - - + +
90B ARG 3.0 11.8 + - - +
91B LEU* 3.4 8.7 - - + +
93B ASN* 1.3 76.2 - - - +
95B LEU* 1.3 72.4 + - + +
97B MET* 3.1 25.6 + - + +
98B MET* 3.4 30.8 + - + +
148B SER* 3.4 27.1 - - - -
152B PHE* 3.5 26.7 - + + -
502B HEM 3.8 31.9 - - + -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LEU* 2.9 43.4 + - + +
92B VAL 3.9 3.1 - - - +
94B PHE* 1.3 90.4 - - + +
96B MET* 1.3 63.6 + - - +
98B MET* 3.2 14.1 + - - +
117B LEU 4.7 1.4 - - - +
119B ALA* 4.3 4.2 - - - +
127B ILE* 4.1 17.7 - - + -
129B MET* 3.4 25.3 - - + +
145B ILE* 4.8 10.8 - - + -
148B SER* 4.5 5.8 - - - -
156B ILE* 5.8 0.2 - - + -
176B ILE* 4.0 25.6 - - + -
178B PHE* 4.1 9.6 - - + -
502B HEM 4.4 26.0 - - + -
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Residues in contact with MET 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.0 33.1 + - + +
93B ASN* 3.7 10.5 - - - +
94B PHE 3.3 0.4 - - - -
95B LEU* 1.3 75.3 - - - +
97B MET* 1.3 59.9 + - - +
98B MET 3.4 0.4 + - - -
99B ASP* 4.6 6.3 + - - +
100B GLU* 5.4 0.9 + - - +
117B LEU 5.8 0.2 - - - +
119B ALA* 3.7 41.8 + - + +
120B LYS* 4.0 6.3 - - - -
121B PRO* 3.9 22.2 - - + -
127B ILE* 4.5 10.8 - - + -
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Residues in contact with MET 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 4.7 12.1 - - - +
89B ARG* 3.4 45.8 - - - +
93B ASN* 3.1 23.8 + - + +
94B PHE* 3.1 17.3 - - - +
96B MET* 1.3 75.4 - - - +
98B MET* 1.3 71.7 + - + +
99B ASP 3.3 2.5 + - - -
100B GLU* 3.3 11.5 + - + +
101B VAL* 3.0 32.5 + - + +
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Residues in contact with MET 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 5.3 1.8 - - + -
94B PHE* 3.4 44.8 + - + +
95B LEU* 3.2 18.0 + - - +
97B MET* 1.3 82.8 - - + +
99B ASP* 1.3 61.9 + - - +
101B VAL* 3.3 21.0 + - + +
102B HIS* 2.7 35.5 + - - -
117B LEU* 4.0 11.0 - - + -
129B MET* 4.0 13.5 - - + -
502B HEM 3.6 60.1 - - + -
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Residues in contact with ASP 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET 4.6 5.7 + - - +
97B MET 3.3 0.4 - - - -
98B MET* 1.3 78.6 - - - +
100B GLU* 1.3 64.4 + - - +
102B HIS* 3.3 3.8 + - - +
103B LEU* 3.2 31.4 + - - +
115B PRO 4.5 0.7 - - - +
116B ARG* 2.8 47.5 + - - +
117B LEU* 2.9 44.4 + - - +
118B ILE* 3.8 13.7 - - + +
119B ALA 5.4 0.7 - - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B MET 5.4 0.8 + - - +
97B MET* 3.3 12.6 + - + +
99B ASP* 1.3 79.7 + - - +
101B VAL* 1.3 58.4 + - + +
103B LEU* 3.3 18.6 + - - +
104B GLN* 2.7 68.5 + - + +
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Residues in contact with VAL 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.8 37.7 - - + -
97B MET* 3.0 26.9 + - + +
98B MET* 3.5 26.7 - - + +
99B ASP 3.3 0.2 - - - -
100B GLU* 1.3 77.5 - - + +
102B HIS* 1.3 65.7 + - - +
104B GLN* 3.3 5.2 + - - +
105B LEU* 2.9 51.4 + - + +
502B HEM 4.3 11.4 - - + -
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Residues in contact with HIS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B MET* 2.7 36.2 + - - +
99B ASP 3.9 3.4 - - - +
101B VAL* 1.3 78.2 - - - +
103B LEU* 1.3 60.5 + - + +
105B LEU* 4.2 4.0 - - - -
106B THR* 2.8 32.7 + - - +
114B PRO* 3.7 8.2 - - + +
115B PRO* 3.9 27.1 - - + +
117B LEU* 3.4 15.3 - - + +
502B HEM 2.0 97.7 + + + -
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ASP* 3.2 32.0 + - - +
100B GLU* 3.6 22.7 - - - +
102B HIS* 1.3 77.4 - - + +
104B GLN* 1.3 66.8 + - + +
106B THR* 3.3 6.3 + - - -
107B LYS* 3.1 27.8 + - + +
114B PRO* 4.1 14.6 - - + -
115B PRO 5.7 0.4 - - - +
116B ARG* 3.9 34.8 - - - +
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Residues in contact with GLN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B TYR* 5.0 8.3 - - - +
100B GLU* 2.7 50.1 + - + +
101B VAL* 3.3 6.5 + - - +
103B LEU* 1.3 81.4 - - - +
105B LEU* 1.3 62.4 + - + +
106B THR 3.4 1.0 + - - -
107B LYS* 3.0 47.2 + - - +
108B MET* 3.5 15.8 - - - +
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 3.8 14.7 + - - -
82B PHE* 4.0 22.4 - - + -
85B TYR* 4.1 18.4 - - + +
101B VAL* 2.9 29.5 + - + +
102B HIS 4.4 2.0 - - - +
103B LEU 3.3 0.2 - - - -
104B GLN* 1.3 77.8 - - + +
106B THR* 1.3 57.8 + - - +
107B LYS 3.7 0.2 - - - -
108B MET* 3.3 20.2 - - + +
502B HEM 3.5 54.1 - - + -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B LYS* 4.2 11.0 - - - +
102B HIS 2.8 23.8 + - - +
103B LEU* 3.3 4.2 + - - -
105B LEU* 1.3 80.2 - - - +
107B LYS* 1.3 66.4 + - - +
108B MET* 3.1 6.5 - - - -
109B ILE* 3.0 19.3 + - + +
112B ALA* 3.5 26.4 - - + +
114B PRO* 3.3 18.6 - - + +
502B HEM 3.9 39.9 - - + +
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Residues in contact with LYS 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU 3.1 14.3 + - - +
104B GLN* 3.0 45.8 + - - +
105B LEU 3.7 0.2 - - - -
106B THR* 1.3 78.3 - - - +
108B MET* 1.3 68.9 - - + +
109B ILE 3.2 3.4 + - - +
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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