Contacts of the helix formed by residues 98 - 117 (chain B) in PDB entry 6S6A
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 GLU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 2.6 36.0 + - - +
96B SER* 3.4 5.2 + - - -
97B ARG* 1.3 72.4 - - + +
99B LEU* 1.3 62.8 + - - +
100B GLU 3.3 2.7 - - - -
101B LYS* 3.3 41.1 + - + +
102B ASP* 3.0 23.1 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASP 5.5 1.3 - - - +
96B SER* 3.5 24.7 - - - +
97B ARG* 2.8 15.4 + - - +
98B GLU* 1.3 70.3 - - - +
100B GLU* 1.3 59.7 + - + +
102B ASP* 3.7 7.1 + - + +
103B MET* 3.1 40.4 + - + +
144B ARG* 3.4 35.0 - - + +
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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
----------------------------------------------------------
98B GLU 3.3 0.4 - - - -
99B LEU* 1.3 76.4 - - + +
101B LYS* 1.3 65.0 + - - +
103B MET* 3.4 8.5 + - - +
104B HIS* 3.2 35.4 + - + +
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 5.8 2.8 - - - +
67B ASP* 2.6 40.2 + - - -
98B GLU* 3.3 43.0 + - + +
100B GLU* 1.3 77.0 - - - +
102B ASP* 1.3 63.8 + - - +
104B HIS* 3.4 11.0 + - + +
105B TYR* 3.2 46.7 + - + -
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 3.1 38.9 + - - +
90B TYR* 4.1 3.8 + - + -
92B PHE* 4.4 17.9 - - + -
93B ASP 5.1 2.1 + - - +
96B SER* 2.6 31.6 + - - -
98B GLU* 3.0 21.8 + - - +
99B LEU* 3.8 7.7 - - - +
101B LYS* 1.3 79.4 - - - +
103B MET* 1.3 61.6 + - + +
105B TYR* 3.3 8.9 + - - +
106B TYR* 3.0 28.4 + - - +
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Residues in contact with MET 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B PHE* 4.1 28.9 - - + -
99B LEU* 3.1 28.1 + - + +
100B GLU* 3.6 12.3 - - - +
102B ASP* 1.3 74.5 - - + +
104B HIS* 1.3 67.7 + - + +
106B TYR* 3.3 10.2 + - - +
107B GLN* 2.9 35.6 + - + +
147B ASP* 6.0 1.8 - - + -
148B LEU* 4.3 12.6 - - + -
151B LEU* 3.7 36.1 - - + -
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Residues in contact with HIS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B GLU* 3.2 28.9 + - + +
101B LYS* 3.4 11.4 + - - +
102B ASP 3.3 0.2 - - - -
103B MET* 1.3 80.6 - - + +
105B TYR* 1.3 60.4 + - + +
107B GLN* 3.3 13.9 + - - +
108B SER* 2.9 34.7 + - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LYS* 6.3 5.2 - - + -
67B ASP* 3.3 32.6 + - - +
70B MET* 3.4 47.1 - - + -
71B GLU* 4.0 15.6 + - + +
74B PHE* 3.8 17.3 - + - -
90B TYR* 3.6 15.5 - - - +
101B LYS* 3.2 48.6 + - + -
102B ASP* 3.3 9.0 + - - +
103B MET 3.2 0.6 - - - -
104B HIS* 1.3 75.7 - - + +
106B TYR* 1.3 66.2 + - - +
108B SER* 3.3 7.1 + - - -
109B CYS* 3.1 26.2 + - - -
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 5.1 0.9 - - + -
90B TYR* 3.4 41.6 + + + -
92B PHE* 3.5 19.3 - + + -
102B ASP 3.0 16.6 + - - +
103B MET* 3.6 12.1 - - - +
105B TYR* 1.3 75.1 - - - +
107B GLN* 1.3 63.0 + - + +
109B CYS* 2.9 9.5 + - - +
110B LEU* 2.8 61.1 + - + +
122B ILE* 4.1 3.5 - - + +
124B CYS* 3.2 31.4 - - - -
148B LEU* 3.8 14.4 - - + -
151B LEU* 4.8 3.1 - - + -
152B SER* 2.8 34.0 + - - -
157B CYS* 4.0 6.1 - - - +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B MET* 2.9 23.1 + - + +
104B HIS* 3.8 15.8 + - - +
106B TYR* 1.3 82.2 - - + +
108B SER* 1.3 52.1 + - - +
110B LEU* 3.2 8.7 + - + +
111B GLU* 2.8 38.3 + - - +
151B LEU* 3.3 33.2 + - + +
404B 9JE 3.2 35.8 + - + +
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Residues in contact with SER 108 (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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74B PHE* 3.5 41.1 - - - -
78B ARG* 4.6 2.6 + - - -
104B HIS* 2.9 17.0 + - - +
105B TYR* 3.5 4.6 - - - -
106B TYR 3.2 0.2 - - - -
107B GLN* 1.3 76.4 - - - +
109B CYS* 1.3 60.1 - - - +
111B GLU* 3.3 11.7 + - - +
112B ALA* 3.2 22.2 + - - +
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Residues in contact with CYS 109 (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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13B MET* 3.8 22.9 - - - -
70B MET* 3.8 17.5 - - - -
74B PHE* 3.9 7.4 - - - -
82B PHE* 3.6 17.9 - - + -
88B LEU* 4.6 6.5 - - + -
90B TYR* 3.7 27.4 - - + -
105B TYR 3.1 17.4 + - - -
106B TYR 2.9 8.7 + - - +
108B SER* 1.3 70.7 - - - +
110B LEU* 1.3 61.6 + - - +
112B ALA 3.5 0.7 + - - -
113B ILE* 3.0 33.0 + - - +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 4.1 13.7 - - + -
106B TYR* 2.8 60.1 + - + +
107B GLN* 3.2 9.4 + - - +
109B CYS* 1.3 77.0 - - - +
111B GLU* 1.3 56.3 + - - +
113B ILE* 3.2 5.3 + - + +
114B LEU* 2.9 29.3 + - - +
122B ILE* 4.0 27.6 - - + -
151B LEU 4.6 1.3 - - - +
152B SER* 3.6 31.4 - - - +
155B LEU* 3.6 16.0 - - + +
404B 9JE 3.8 9.9 - - + -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ARG* 3.9 16.1 + - - +
107B GLN 2.8 18.0 + - - +
108B SER* 3.6 9.0 - - - +
110B LEU* 1.3 73.9 - - - +
112B ALA* 1.3 57.8 + - - +
114B LEU* 3.4 5.1 + - + +
115B GLN* 3.1 30.8 + - + +
404B 9JE 4.1 36.2 + - + +
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Residues in contact with ALA 112 (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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74B PHE* 5.4 0.4 - - + -
78B ARG* 3.3 29.1 - - - +
82B PHE* 3.5 39.4 - - + +
108B SER 3.2 11.5 + - - +
109B CYS 3.7 3.8 - - - +
110B LEU 3.3 0.2 - - - -
111B GLU* 1.3 73.9 - - - +
113B ILE* 1.4 62.5 + - - +
115B GLN* 3.4 1.0 + - - -
116B ASN* 2.7 33.7 + - - +
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Residues in contact with ILE 113 (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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11B LEU* 4.5 2.0 - - + -
82B PHE* 3.8 17.9 - - + +
85B VAL* 4.0 33.0 - - + -
88B LEU* 4.0 25.8 - - + -
109B CYS 3.0 19.7 + - - +
110B LEU* 3.2 9.8 + - - +
112B ALA* 1.4 72.9 - - - +
114B LEU* 1.3 60.9 + - - +
117B SER* 2.7 53.6 + - - +
118B PRO* 4.7 0.2 - - + -
120B ALA* 4.0 14.6 - - + +
122B ILE* 4.3 6.7 - - + -
155B LEU* 4.1 18.8 - - + -
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Residues in contact with LEU 114 (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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110B LEU 2.9 13.0 + - - +
111B GLU* 3.5 9.2 - - - +
113B ILE* 1.3 76.4 - - - +
115B GLN* 1.3 62.5 + - - +
118B PRO* 3.4 30.9 - - + +
154B PRO* 4.5 19.5 - - + -
155B LEU* 4.0 24.5 - - + -
404B 9JE 3.8 26.9 - - + -
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Residues in contact with GLN 115 (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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78B ARG* 2.9 47.2 + - - +
111B GLU* 3.1 15.2 + - + +
112B ALA 3.5 2.7 - - - +
113B ILE 3.2 0.2 - - - -
114B LEU* 1.3 79.2 - - - +
116B ASN* 1.3 75.2 + - - +
118B PRO* 4.5 3.5 - - - +
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Residues in contact with ASN 116 (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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78B ARG* 4.3 13.8 - - - +
79B ASP* 3.2 25.1 - - - +
82B PHE* 3.0 31.8 - - - +
83B ARG* 3.8 17.9 + - + +
84B ASN 4.4 1.9 + - - -
112B ALA* 2.7 27.5 + - - +
115B GLN* 1.3 99.2 + - - +
117B SER* 1.3 61.2 + - - +
118B PRO* 3.5 7.6 - - - +
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Residues in contact with SER 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PHE 2.8 22.0 + - - -
84B ASN* 3.2 9.5 + - - -
85B VAL* 3.0 44.8 + - - -
113B ILE* 2.7 20.9 + - - +
116B ASN* 1.3 69.3 + - - +
118B PRO* 1.3 55.6 - - - +
119B ASP 2.7 17.2 + - - -
120B ALA* 2.8 18.6 + - - +
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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