Contacts of the helix formed by residues 94 - 110 (chain B) in PDB entry 3NYO
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 94 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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555A LEU* 3.8 28.5 - - + +
556A PHE* 4.5 11.9 - - + -
92B VAL 3.7 8.1 - - - +
93B THR* 1.3 91.7 - - + +
95B ASP* 1.3 61.5 + - - +
96B ASP* 3.2 21.5 - - - +
97B LYS* 3.1 7.4 + - + +
98B ARG 2.9 23.2 + - - -
455B ARG* 3.5 25.8 - - - +
579B SO4 3.5 13.7 - - - +
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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
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94B PRO* 1.3 66.6 - - - +
96B ASP* 1.3 58.7 + - - +
97B LYS 3.0 10.4 + - - -
98B ARG* 3.1 35.7 + - - +
99B LYS* 4.6 4.5 + - - +
579B SO4 2.9 31.9 + - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B PRO* 3.6 18.9 - - - +
95B ASP* 1.3 76.7 + - - +
97B LYS* 1.3 85.5 + - - +
99B LYS* 6.3 1.1 - - - -
455B ARG* 5.4 0.2 + - - -
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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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554A ARG 5.3 3.6 + - - +
555A LEU* 3.9 12.4 + - - +
556A PHE* 2.9 41.4 + - - +
557A SER* 5.4 1.0 - - - -
93B THR* 4.0 15.5 - - + -
94B PRO* 3.1 8.6 + - + +
95B ASP 3.0 0.4 - - - -
96B ASP* 1.3 97.2 - - - +
98B ARG* 1.3 69.6 + - - +
99B LYS* 3.3 3.4 - - - -
100B ALA* 2.9 24.3 + - + +
101B CYS* 3.0 12.4 + - + +
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Residues in contact with ARG 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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90B TYR* 3.8 37.3 + - + +
91B GLU 5.0 6.5 + - - -
93B THR* 3.0 28.7 + - - +
94B PRO 2.9 11.2 + - - +
95B ASP* 3.1 44.9 + - - +
97B LYS* 1.3 75.6 - - - +
99B LYS* 1.3 59.3 + - - +
101B CYS* 3.2 2.4 + - - +
102B GLY* 2.8 27.5 + - - -
137B PRO* 3.5 30.4 + - + +
138B CYS* 4.3 0.6 - - - +
139B LYS* 4.0 36.2 - - - +
454B LYS* 4.4 7.7 - - - +
579B SO4 3.4 13.9 + - - -
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Residues in contact with LYS 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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95B ASP 4.6 5.0 + - - +
96B ASP 6.3 0.7 - - - -
97B LYS 3.2 1.8 + - - -
98B ARG* 1.3 79.8 - - - +
100B ALA* 1.3 60.5 + - + +
102B GLY* 3.4 2.1 + - - +
103B ARG* 3.0 61.5 + - - +
133B LEU* 4.7 7.3 - - + +
134B GLU* 6.0 4.0 - - - +
137B PRO* 4.1 26.7 - - + +
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Residues in contact with ALA 100 (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* 2.9 15.1 + - + +
99B LYS* 1.3 83.3 - - + +
101B CYS* 1.3 61.5 + - - +
103B ARG* 3.5 9.7 + - - +
104B GLN* 3.2 21.3 + - - +
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Residues in contact with CYS 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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86B GLY 5.5 0.4 - - - -
89B GLU* 4.7 18.2 - - - -
90B TYR* 4.6 16.4 - - + -
93B THR* 4.3 25.4 - - + +
97B LYS* 3.0 10.8 + - + +
98B ARG* 3.6 7.9 - - - +
100B ALA* 1.3 74.2 - - - +
102B GLY* 1.3 64.1 + - - +
104B GLN* 3.4 21.1 + - - +
105B LEU* 3.4 17.2 + - - +
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Residues in contact with GLY 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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90B TYR* 3.7 22.2 - - - -
98B ARG 2.8 17.1 + - - -
99B LYS* 3.7 2.7 - - - -
100B ALA 3.3 0.2 - - - -
101B CYS* 1.3 76.8 - - - +
103B ARG* 1.3 54.0 + - - +
105B LEU* 3.3 8.5 + - - +
106B THR* 2.7 29.6 + - - -
133B LEU* 4.4 10.8 - - - -
142B PHE* 4.3 7.5 - - - -
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Residues in contact with ARG 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 LYS* 3.0 47.1 + - - +
100B ALA* 3.8 8.7 - - - +
101B CYS 3.3 0.2 - - - -
102B GLY* 1.3 72.3 - - - +
104B GLN* 1.3 66.0 + - - +
106B THR* 3.1 19.1 + - - -
107B GLN* 3.1 34.8 + - - +
133B LEU* 4.5 17.2 - - + +
134B GLU* 4.0 36.8 + - - +
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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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100B ALA 3.2 11.9 + - - +
101B CYS* 3.4 16.6 - - - +
103B ARG* 1.3 76.9 - - - +
105B LEU* 1.3 65.0 + - + +
107B GLN* 4.1 4.6 + - - -
108B ASN* 2.7 50.3 + - - +
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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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83B PHE* 5.2 5.8 - - + +
86B GLY* 3.8 40.8 - - - +
87B VAL* 3.8 12.8 - - + +
89B GLU* 6.0 0.7 - - - +
90B TYR* 4.3 13.0 - - + -
101B CYS* 3.6 18.4 - - - +
102B GLY 3.3 6.4 + - - +
103B ARG 3.1 0.8 - - - -
104B GLN* 1.3 83.3 - - + +
106B THR* 1.3 67.0 + - - +
107B GLN 3.2 0.2 - - - -
108B ASN* 2.9 1.8 + - + -
109B PHE* 2.8 54.7 + - + +
110B LEU* 5.3 1.8 - - + -
142B PHE* 4.6 18.4 - - + -
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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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102B GLY 2.7 23.2 + - - -
103B ARG* 3.1 12.6 + - - -
105B LEU* 1.3 76.1 - - - +
107B GLN* 1.3 61.9 + - + +
110B LEU* 3.0 57.1 + - + +
111B SER* 3.5 0.3 + - - -
130B THR* 4.7 17.9 - - + +
133B LEU* 4.1 23.7 - - + +
142B PHE* 5.0 5.3 - - + -
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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
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103B ARG* 3.1 34.0 + - - +
104B GLN* 5.0 2.6 - - - -
106B THR* 1.3 83.7 - - + +
108B ASN* 1.3 68.4 + - - +
111B SER* 3.7 22.1 + - - +
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Residues in contact with ASN 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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79B ARG* 3.5 12.0 + - - -
104B GLN* 2.7 41.5 + - - +
105B LEU* 2.9 6.0 + - - +
107B GLN* 1.3 88.2 + - - +
109B PHE* 1.3 79.3 + - + +
110B LEU 3.6 0.2 - - - -
111B SER* 4.5 5.8 + - - -
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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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79B ARG* 3.5 42.9 + - + +
82B ALA* 3.8 16.6 - - + -
83B PHE* 3.5 67.1 - + + -
86B GLY* 5.8 0.2 - - - -
105B LEU* 2.8 41.9 + - + +
108B ASN* 1.3 90.7 - - + +
110B LEU* 1.3 65.0 + - + +
111B SER 3.7 2.8 - - - +
115B PRO 5.2 1.4 - - - +
117B LEU* 4.5 19.4 + - + +
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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
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83B PHE* 4.7 8.3 - - + -
105B LEU 5.0 1.3 - - - +
106B THR* 3.0 38.8 + - + +
109B PHE* 1.3 87.4 - - + +
111B SER* 1.3 63.7 + - - +
112B HIS* 3.5 6.4 + - - -
117B LEU* 5.4 8.7 - - + -
126B VAL* 4.3 37.4 - - + +
129B CYS* 5.4 7.2 - - + -
142B PHE* 4.4 16.4 - - + -
145B LEU* 4.1 35.2 - - + -
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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
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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