Contacts of the helix formed by residues 89 - 108 (chain B) in PDB entry 3SEA
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 89 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 4.4 7.0 - - - -
17B VAL* 5.8 0.4 - - - -
86B SER* 3.1 14.2 + - - +
87B VAL 3.5 1.0 - - - -
88B THR* 1.3 81.2 + - - +
90B ILE* 1.3 62.8 + - - +
91B LYS* 3.4 10.4 + - - +
92B SER* 2.6 52.7 + - - -
93B PHE* 3.5 2.3 + - - +
128B VAL* 3.8 2.2 - - - +
129B ILE* 4.1 3.8 - - - +
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B SER* 1.3 71.4 - - - +
91B LYS* 1.3 65.4 + - - +
93B PHE* 2.9 15.2 + - + +
94B GLU* 3.1 14.2 + - + +
128B VAL* 3.7 29.4 - - + +
129B ILE* 3.9 16.4 - - + -
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Residues in contact with LYS 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.7 31.6 - - + +
66B GLU* 3.0 35.8 + - - -
89B SER* 3.2 8.0 + - - +
90B ILE* 1.3 78.9 - - - +
92B SER* 1.3 56.3 + - - +
94B GLU* 2.8 38.2 + - - +
95B VAL* 2.9 38.3 + - - +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.9 18.5 - - - +
17B VAL* 3.6 31.4 - - - -
84B VAL 5.0 0.3 - - - +
85B TYR* 3.5 4.9 - - - +
86B SER 3.0 22.6 + - - -
89B SER* 2.6 35.4 + - - -
91B LYS* 1.3 77.1 - - - +
93B PHE* 1.3 56.9 + - - +
95B VAL* 3.8 1.7 - - - +
96B ILE* 3.0 28.2 + - - +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TYR* 3.7 44.6 - + + -
89B SER 4.3 5.2 - - - +
90B ILE* 2.9 11.4 + - + +
92B SER* 1.3 79.5 + - - +
94B GLU* 1.3 66.2 + - - +
96B ILE* 3.1 23.0 - - + +
97B LYS* 3.3 22.9 + - + +
129B ILE* 3.8 24.7 - - + -
133B GLU* 3.5 27.1 - - + -
134B GLY* 4.0 8.5 - - - -
137B LEU* 3.6 27.4 - - + -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 4.1 10.9 - - - +
90B ILE* 3.1 13.8 + - + +
91B LYS* 2.8 43.0 + - - +
93B PHE* 1.3 76.8 - - - +
95B VAL* 1.3 63.1 - - - +
97B LYS* 3.4 13.9 + - - +
98B VAL* 3.4 25.6 + - + +
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Residues in contact with VAL 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.7 27.4 - - + -
64B GLN 3.4 24.9 - - - +
65B ASP* 4.0 9.6 - - - -
66B GLU* 4.1 14.8 - - + +
91B LYS* 2.9 39.8 + - - +
92B SER 3.8 3.4 - - - +
94B GLU* 1.3 76.5 - - + +
96B ILE* 1.3 61.1 + - - +
98B VAL* 3.0 9.0 + - + +
99B ILE* 2.8 40.0 + - + +
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Residues in contact with ILE 96 (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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12B LEU 4.0 0.2 - - - +
13B GLY* 3.9 16.4 - - - -
14B TYR 5.0 0.4 - - - +
83B LEU* 3.4 43.1 - - + -
84B VAL 3.5 25.8 - - - +
85B TYR* 4.5 7.4 - - + -
92B SER 3.0 14.6 + - - +
93B PHE* 3.1 27.1 - - + +
95B VAL* 1.3 76.7 - - - +
97B LYS* 1.3 64.5 + - - +
99B ILE* 3.8 6.5 - - + +
100B HIS* 2.9 24.4 + - - +
116B LEU* 4.2 15.3 - - + -
137B LEU* 4.3 17.9 - - + -
141B TRP* 3.9 1.1 - - + -
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Residues in contact with LYS 97 (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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93B PHE* 3.3 32.7 + - + +
94B GLU* 3.6 11.7 - - - +
95B VAL 3.1 0.4 - - - -
96B ILE* 1.3 83.3 - - - +
98B VAL* 1.3 57.5 + - + +
100B HIS* 3.5 4.0 + - - +
101B GLY* 3.1 22.9 + - - -
137B LEU* 3.7 35.2 - - + +
141B TRP* 4.2 7.6 - - + +
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Residues in contact with VAL 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP 5.1 1.3 - - - +
66B GLU* 4.3 26.2 - - + +
94B GLU* 3.4 19.5 + - + +
95B VAL* 3.0 11.3 + - + +
97B LYS* 1.3 75.9 - - + +
99B ILE* 1.3 67.6 + - + +
101B GLY* 3.2 2.8 + - - -
102B LYS* 3.0 49.8 + - + +
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Residues in contact with ILE 99 (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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12B LEU* 4.2 17.9 - - + -
13B GLY* 3.6 39.7 - - - +
64B GLN* 4.0 26.0 - - + +
65B ASP 5.4 2.5 - - - +
68B SER* 5.3 0.2 - - - +
70B PHE* 4.1 20.8 - - + -
83B LEU* 4.3 10.5 - - + -
95B VAL* 2.8 36.0 + - + +
96B ILE* 3.8 9.2 - - + +
98B VAL* 1.3 79.4 - - + +
100B HIS* 1.3 57.9 + - - +
102B LYS* 3.3 9.5 + - + +
103B LEU* 2.8 27.6 + - + +
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Residues in contact with HIS 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 3.6 11.9 - - + +
96B ILE 2.9 11.3 + - - +
97B LYS 3.7 3.0 + - - +
99B ILE* 1.3 78.3 - - - +
101B GLY* 1.3 65.6 + - - +
103B LEU* 3.1 7.4 + - + +
104B LEU* 2.9 60.6 + - + +
114B ILE* 4.1 19.5 - - + +
141B TRP* 3.4 78.5 + + + +
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Residues in contact with GLY 101 (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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97B LYS 3.1 15.0 + - - -
98B VAL 3.2 3.7 + - - -
100B HIS* 1.3 79.5 + - - +
102B LYS* 1.3 56.2 + - - +
104B LEU* 3.4 7.6 + - - +
105B ASP* 3.0 36.7 + - - +
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Residues in contact with LYS 102 (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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64B GLN* 5.2 1.6 - - - +
65B ASP 3.8 4.8 + - - -
66B GLU 2.8 30.4 + - - -
67B TYR 4.2 0.4 - - - -
68B SER* 2.6 32.9 + - - +
70B PHE* 3.9 26.0 - - + +
98B VAL* 3.0 29.6 + - + +
99B ILE* 3.6 10.1 - - - +
101B GLY* 1.3 73.4 - - - +
103B LEU* 1.3 67.7 + - - +
105B ASP* 3.2 13.2 + - - +
106B MET* 3.0 28.1 + - + +
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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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12B LEU* 4.7 2.0 - - + -
70B PHE* 3.6 34.0 - - + -
74B TYR 4.4 0.2 - - - +
81B TYR* 3.6 54.1 - - + +
83B LEU* 4.3 16.4 - - + -
99B ILE* 2.8 14.2 + - + +
100B HIS* 3.4 11.9 - - + +
102B LYS* 1.3 77.1 - - - +
104B LEU* 1.3 66.9 + - + +
106B MET* 3.0 13.0 + - - +
107B VAL* 3.1 29.6 + - + +
112B ILE* 5.3 1.1 - - + -
114B ILE* 4.4 15.0 - - + -
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Residues in contact with LEU 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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100B HIS* 2.9 56.3 + - + +
101B GLY* 3.7 7.4 - - - +
103B LEU* 1.3 77.6 - - + +
105B ASP* 1.3 68.2 + - - +
107B VAL* 3.9 13.5 - - + -
108B GLY* 3.0 32.0 + - - +
110B VAL 5.7 2.5 - - - +
112B ILE* 5.6 2.0 - - + -
114B ILE* 4.8 8.7 - - + -
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Residues in contact with ASP 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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101B GLY 3.0 22.9 + - - +
102B LYS* 3.2 14.0 + - - +
104B LEU* 1.3 78.1 - - - +
106B MET* 1.3 64.5 + - + +
108B GLY* 4.5 2.3 + - - -
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Residues in contact with MET 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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69B ILE* 6.2 1.1 - - + -
70B PHE* 3.5 50.3 - - + +
72B GLN* 4.1 17.5 - - - +
75B SER* 3.2 38.5 + - - +
102B LYS* 3.0 16.4 + - + +
103B LEU* 3.0 11.2 + - - +
105B ASP* 1.3 83.3 - - + +
107B VAL* 1.3 59.9 + - - +
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Residues in contact with VAL 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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75B SER* 3.8 27.1 - - - +
81B TYR* 4.0 2.9 - - - +
103B LEU* 3.3 34.8 - - + +
104B LEU* 3.8 12.1 - - + +
106B MET* 1.3 82.4 - - - +
108B GLY* 1.3 72.8 + - - +
110B VAL* 3.3 14.5 - - + +
112B ILE* 3.3 33.0 - - + -
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Residues in contact with GLY 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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104B LEU* 3.0 21.2 + - - +
105B ASP 4.5 2.1 + - - -
106B MET 3.9 0.4 - - - -
107B VAL* 1.3 91.7 - - - +
109B LYS* 1.3 57.0 - - - -
110B VAL* 2.8 16.6 + - - +
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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
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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