Contacts of the helix formed by residues 92 - 111 (chain B) in PDB entry 4IYM
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 THR 92 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B SER* 3.4 1.2 + - - -
90B GLY 4.8 0.2 - - - -
91B LYS* 1.3 79.2 - - - +
93B ILE* 1.3 58.0 + - - +
94B ASP* 3.5 9.3 + - - +
95B ASP* 3.0 36.0 + - - +
96B ALA 2.9 24.4 + - - -
310B GLY 5.8 0.4 - - - +
312B TYR* 4.6 10.1 - - - +
314B ASP 5.6 2.9 - - - +
315B GLU* 6.4 1.8 - - - -
317B ALA* 3.6 29.4 - - + +
318B ASP 4.1 3.4 - - - +
319B MSE 4.1 23.3 - - - +
320B GLY* 4.6 1.1 - - - +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ASN 5.4 0.4 - - - +
82B ALA* 3.5 24.9 - - + +
83B GLU* 3.8 12.6 - - + +
86B SER* 3.5 21.0 + - - +
91B LYS 3.8 0.2 + - - -
92B THR* 1.3 72.3 - - - +
94B ASP* 1.3 57.4 + - - +
96B ALA* 3.1 3.0 + - - +
97B LYS* 2.8 54.8 + - + +
312B TYR* 3.8 30.8 + - + +
315B GLU* 4.1 24.5 - - + +
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.2 8.9 - - - +
93B ILE* 1.3 80.2 - - - +
95B ASP* 1.3 63.9 + - - +
97B LYS* 3.4 12.0 + - - +
98B GLY* 3.0 19.1 + - - -
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Residues in contact with ASP 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B LYS* 3.7 25.3 + - + +
92B THR* 3.0 42.5 + - - +
94B ASP* 1.3 76.2 - - - +
96B ALA* 1.3 59.0 + - - +
98B GLY* 3.2 3.0 + - - +
99B ASP* 2.9 28.2 + - - +
149B PHE* 5.6 0.7 - - - -
273B GLY* 5.6 1.4 - - - -
274B SER* 4.0 26.0 + - - +
318B ASP 4.8 3.0 - - - +
319B MSE 5.7 0.5 - - - -
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Residues in contact with ALA 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 3.6 22.2 - - - +
85B LEU* 3.9 16.8 - - + +
86B SER* 3.3 24.9 - - - +
91B LYS* 4.2 5.8 - - + +
92B THR 2.9 7.2 + - - +
93B ILE 3.6 5.2 - - - +
95B ASP* 1.3 75.0 - - - +
97B LYS* 1.3 57.3 + - - +
99B ASP* 3.3 9.1 - - - +
100B ILE* 3.0 33.7 + - - +
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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
----------------------------------------------------------
78B MSE 4.0 27.7 - - + +
79B ASN* 3.1 30.5 - - - +
82B ALA* 3.8 15.3 - - + -
93B ILE* 2.8 37.6 + - + +
94B ASP* 3.7 14.1 - - - +
96B ALA* 1.3 72.6 - - - +
98B GLY* 1.3 54.5 + - - +
100B ILE* 3.1 3.2 + - - +
101B VAL* 2.8 43.6 + - + +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ASP 3.0 14.2 + - - -
95B ASP* 3.2 4.5 + - - -
97B LYS* 1.3 72.8 - - - +
99B ASP* 1.3 61.7 + - - +
101B VAL* 3.3 5.7 + - - +
102B ARG* 3.0 38.4 + - - +
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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
----------------------------------------------------------
85B LEU* 3.5 10.5 - - + +
91B LYS* 2.8 30.1 + - - +
95B ASP 2.9 15.7 + - - +
96B ALA 3.3 10.5 - - - +
97B LYS 3.2 0.2 - - - -
98B GLY* 1.3 72.2 - - - +
100B ILE* 1.3 61.5 + - - +
102B ARG* 3.5 1.6 + - - +
103B GLY 3.4 5.5 + - - -
149B PHE* 3.2 35.3 - - + -
150B PRO* 3.3 9.4 - - - +
151B GLY* 3.2 5.5 + - - -
152B MSE 2.7 50.7 + - - +
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Residues in contact with ILE 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.8 10.8 - - + -
78B MSE 3.8 28.7 - - + -
81B LEU* 4.2 38.6 - - + -
82B ALA 4.8 3.6 - - - +
85B LEU* 3.8 21.8 - - + -
96B ALA 3.0 16.7 + - - +
97B LYS 3.6 5.2 - - - +
99B ASP* 1.3 75.4 - - - +
101B VAL* 1.3 58.0 + - - +
103B GLY* 3.0 4.5 + - - -
104B LEU* 2.8 24.7 + - + +
151B GLY* 4.2 14.1 - - - -
155B MSE 3.6 15.4 - - + +
179B VAL* 4.3 9.4 - - + -
183B LEU* 5.2 0.2 - - + -
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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
----------------------------------------------------------
75B ASN* 6.0 0.2 - - - +
78B MSE 3.7 24.0 - - + -
97B LYS* 2.8 28.8 + - + +
98B GLY* 4.0 5.8 - - - +
100B ILE* 1.3 72.9 - - - +
102B ARG* 1.3 60.4 + - + +
104B LEU* 3.0 15.7 + - + +
105B GLU* 3.0 45.1 + - + +
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Residues in contact with ARG 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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98B GLY* 3.0 22.4 + - - +
99B ASP 4.0 0.2 - - - +
101B VAL* 1.3 77.6 - - + +
103B GLY* 1.3 61.7 + - - +
105B GLU* 3.6 22.7 + - - +
106B VAL* 3.7 15.1 + - - +
149B PHE* 4.5 9.0 - - - -
152B MSE 3.5 46.7 - - + +
156B TRP* 4.7 2.2 + - - +
278B ARG* 3.4 33.1 - - - +
441B VAL* 3.9 31.1 - - - +
443B LEU* 6.1 3.8 - - - -
444B ALA* 5.2 0.9 - - - +
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Residues in contact with GLY 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP 3.4 5.7 + - - -
100B ILE 3.0 7.6 + - - -
102B ARG* 1.3 75.4 - - - +
104B LEU* 1.3 66.0 + - - +
106B VAL* 3.1 16.9 + - - +
107B CYS* 3.3 13.5 + - - -
152B MSE 3.9 11.7 - - - +
155B MSE 3.6 32.7 - - - +
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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
----------------------------------------------------------
71B VAL* 3.9 25.7 - - + +
74B LEU* 3.9 29.2 - - + -
75B ASN* 3.6 24.5 - - - +
78B MSE 4.4 11.4 - - + -
100B ILE 2.8 12.8 + - - +
101B VAL* 3.0 21.3 + - + +
103B GLY* 1.3 77.2 - - - +
105B GLU* 1.3 60.5 + - + +
107B CYS* 3.1 8.4 + - - +
108B GLU* 2.9 52.8 + - + +
155B MSE 3.9 0.6 - - - -
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Residues in contact with GLU 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 VAL* 3.0 32.8 + - + +
102B ARG* 3.9 16.4 - - - +
103B GLY 3.1 0.6 - - - -
104B LEU* 1.3 79.5 - - + +
106B VAL* 1.3 59.1 + - - +
108B GLU* 3.4 23.4 + - - +
109B PHE* 3.0 21.3 + - - +
443B LEU* 4.0 22.5 - - - +
444B ALA* 3.3 21.7 + - + +
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Residues in contact with VAL 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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102B ARG 3.7 10.5 + - - +
103B GLY 3.1 7.7 + - - +
105B GLU* 1.3 74.3 - - - +
107B CYS* 1.3 63.1 + - - +
109B PHE* 3.1 7.4 + - + +
110B VAL* 3.0 25.6 + - + +
155B MSE 4.0 8.5 - - - +
156B TRP* 3.6 36.8 - - + +
159B ALA* 3.8 4.7 - - + -
160B PRO* 3.8 29.2 - - + -
444B ALA* 3.7 16.2 - - + -
462B HIS* 4.3 18.4 - - + -
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Residues in contact with CYS 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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67B PHE* 3.8 14.6 - - + +
70B PHE* 3.7 32.8 - - + -
71B VAL* 3.6 19.1 - - + -
103B GLY 3.3 11.2 + - - -
104B LEU* 3.1 13.1 + - - +
106B VAL* 1.3 78.1 - - - +
108B GLU* 1.3 58.0 + - - +
110B VAL* 3.3 22.5 - - - +
111B ILE* 3.4 12.6 + - - +
155B MSE 4.1 11.7 - - - -
158B PHE* 5.0 1.1 - - - -
159B ALA* 4.1 15.0 - - - -
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Residues in contact with GLU 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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71B VAL* 4.1 16.7 - - + +
104B LEU* 2.9 33.7 + - + +
105B GLU* 3.6 27.1 - - - +
106B VAL 3.2 0.4 - - - -
107B CYS* 1.3 72.0 - - - +
109B PHE* 1.3 67.6 + - - +
111B ILE* 3.1 31.5 + - + +
112B GLY 4.2 0.3 + - - -
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Residues in contact with PHE 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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105B GLU 3.0 14.3 + - - +
106B VAL* 3.4 13.7 - - + +
108B GLU* 1.3 76.8 - - - +
110B VAL* 1.3 66.9 + - + +
112B GLY* 3.0 17.7 + - - -
116B LEU* 3.5 44.2 - - + +
444B ALA* 3.8 18.4 - - + -
445B TYR* 3.7 33.2 - - + +
462B HIS* 5.1 0.4 - - + -
463B GLY* 3.3 42.6 - - - -
464B THR* 4.0 3.4 - - + -
466B SER* 4.4 5.4 - - - -
467B ILE* 4.6 6.3 - - + -
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Residues in contact with VAL 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 4.6 1.7 - - - +
67B PHE* 3.7 31.5 - - + -
106B VAL* 3.0 18.4 + - + +
107B CYS* 3.3 16.2 - - - +
109B PHE* 1.3 85.5 - - + +
111B ILE* 1.3 66.3 + - - +
112B GLY 2.9 1.3 - - - -
113B ILE* 3.0 24.4 + - + +
116B LEU* 4.4 5.6 - - - -
159B ALA* 3.8 7.6 - - + +
160B PRO* 3.7 37.9 - - + -
163B ALA* 3.7 10.5 - - + +
467B ILE* 4.8 5.2 - - + -
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Residues in contact with ILE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 3.3 24.0 - - + +
67B PHE* 4.2 3.1 - - + +
68B MSE 3.4 62.4 - - + +
71B VAL* 4.9 5.8 - - + -
107B CYS 3.4 12.8 + - - +
108B GLU* 3.1 30.0 + - + +
110B VAL* 1.3 76.3 - - - +
112B GLY* 1.3 55.0 + - - +
113B ILE 3.1 4.9 + - - -
114B PRO* 3.4 5.2 - - - +
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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