Contacts of the helix formed by residues 83 - 93 (chain B) in PDB entry 2NYM
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 PRO 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81B ILE* 4.4 1.3 - - + +
82B TYR* 1.4 82.6 - - - +
84B GLU* 1.3 58.9 + - + +
85B VAL* 3.0 8.7 - - + +
86B VAL* 4.0 13.3 - - + +
87B HIS* 3.5 20.1 + - - +
134B PHE* 6.4 1.1 - - + -
144B ILE 5.1 3.6 - - - +
148B TYR* 3.2 65.5 - - + +
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Residues in contact with GLU 84 (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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36B LEU* 3.5 34.2 - - + +
39B CYS* 4.4 17.0 - - + +
40B CYS* 3.7 20.1 + - - +
43B PHE* 5.5 0.9 - - - +
82B TYR* 3.4 19.3 + - + -
83B PRO* 1.3 77.8 - - + +
85B VAL* 1.3 59.9 + - - +
87B HIS* 4.3 14.3 - - - +
88B MSE 2.9 28.8 + - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 5.6 2.0 - - - -
66B MSE 5.6 2.9 - - + -
82B TYR* 4.2 30.7 - - + +
83B PRO* 4.8 1.3 - - + -
84B GLU* 1.3 76.7 - - - +
86B VAL* 1.3 66.3 - - - +
88B MSE 3.0 9.0 - - - +
89B PHE* 2.8 23.0 + - - +
130B PHE* 3.2 43.3 - - + -
131B PHE* 4.3 6.1 - - + -
134B PHE* 3.2 43.5 - - + -
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Residues in contact with VAL 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B PRO* 3.8 15.1 + - + +
85B VAL* 1.3 77.5 - - - +
87B HIS* 1.3 69.5 + - - +
89B PHE* 2.6 20.7 + - - +
90B ALA* 2.8 15.4 + - + -
131B PHE* 4.2 12.1 - - + -
134B PHE* 4.9 6.7 - - + -
144B ILE 6.0 0.9 - - - +
145B ALA* 5.6 2.0 - - + -
148B TYR* 3.3 27.6 - - + +
149B ILE* 3.6 31.4 - - + -
153B PHE* 4.5 19.1 - - + -
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Residues in contact with HIS 87 (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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43B PHE* 5.1 9.6 - - + +
44B ASP* 6.1 1.8 + - - +
83B PRO 3.5 14.5 + - - +
84B GLU* 4.3 15.7 - - - +
85B VAL 3.5 0.2 - - - -
86B VAL* 1.3 83.1 - - - +
88B MSE 1.3 60.6 - - - +
89B PHE 3.3 0.2 + - - -
90B ALA* 3.3 9.2 + - - +
91B VAL* 2.7 49.7 - - + +
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Residues in contact with MSE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B CYS* 4.2 12.8 - - + +
42B LEU* 3.7 10.3 - - + +
43B PHE* 3.9 30.2 - - + -
63B LEU* 3.7 25.1 - - + -
66B MSE 6.3 0.9 - - - +
84B GLU 2.9 21.0 + - - +
85B VAL* 3.0 10.5 + - - +
86B VAL 3.0 0.2 - - - -
87B HIS* 1.3 79.7 - - - +
89B PHE* 1.3 60.8 + - - +
91B VAL* 3.3 8.2 - - - +
92B ASN* 2.7 46.4 + - - +
127B VAL* 3.5 34.3 - - + -
130B PHE* 4.4 20.6 - - + -
131B PHE* 6.5 0.2 - - - -
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Residues in contact with PHE 89 (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 VAL 2.8 11.3 + - - +
86B VAL* 2.6 13.6 + - - +
88B MSE 1.3 75.3 - - - +
90B ALA* 1.3 55.8 + - - +
91B VAL 2.5 19.0 + - - -
92B ASN* 2.9 11.3 + - - -
93B MSE 3.0 39.1 + - + +
94B PHE* 3.5 19.5 - + - -
127B VAL* 3.8 12.6 - - + -
128B TYR* 3.8 21.5 - + - -
131B PHE* 3.6 45.8 - + + -
153B PHE* 3.4 32.8 - + - -
157B LEU* 3.9 20.6 - - + -
175B THR* 5.1 1.1 - - + -
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Residues in contact with ALA 90 (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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86B VAL* 2.8 20.5 + - + +
87B HIS* 4.0 5.3 + - - +
89B PHE* 1.3 71.7 - - - +
91B VAL* 1.3 67.5 + - - +
94B PHE* 3.4 51.2 - - + +
153B PHE* 4.1 10.1 - - + -
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Residues in contact with VAL 91 (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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43B PHE* 5.0 1.8 - - + +
44B ASP* 4.8 20.6 - - + +
87B HIS* 2.7 47.1 - - + +
88B MSE 3.3 10.3 - - - +
89B PHE 2.5 9.1 + - - -
90B ALA* 1.3 79.7 - - - +
92B ASN* 1.3 63.7 + - - +
93B MSE 3.3 1.9 - - - +
94B PHE 4.5 10.0 + - - +
95B ARG* 5.7 1.7 - - - +
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Residues in contact with ASN 92 (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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42B LEU 3.9 5.9 + - - +
43B PHE* 4.2 8.1 + - - +
46B VAL* 5.1 3.6 + - - -
59B LYS* 2.8 28.9 + - - -
88B MSE 2.7 49.6 + - - +
89B PHE 2.9 1.8 + - - +
91B VAL* 1.3 80.0 - - - +
93B MSE 1.3 61.9 + - - +
95B ARG* 4.7 7.2 + - - +
123B HIS* 5.3 0.3 - - - -
124B LEU* 3.0 29.0 - - + +
127B VAL* 3.8 25.2 - - + +
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Residues in contact with MSE 93 (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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89B PHE* 3.0 41.5 + - + +
92B ASN* 1.3 84.7 - - - +
94B PHE* 1.3 76.3 + - + +
95B ARG* 2.9 40.5 + - - +
124B LEU* 4.0 20.2 - - + -
127B VAL* 4.5 9.9 - - + -
128B TYR* 3.0 51.8 - - + +
160B LEU* 3.4 12.4 - - + +
168B GLU* 3.3 14.4 - - - +
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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
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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