Contacts of the helix formed by residues 77 - 90 (chain A) 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 ASN 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 2.7 38.1 + - - +
74A LEU 3.2 2.2 + - - -
76A ASP* 1.3 80.8 - - - +
78A MSE 1.3 58.5 + - - +
79A ASN 3.5 2.0 - - - -
80A GLU* 3.3 21.1 + - - +
81A LEU* 2.9 40.9 + - + +
182A ARG* 3.2 24.5 + - - +
186A LEU* 3.5 22.5 - - + +
189A GLU* 5.5 1.4 + - - -
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Residues in contact with MSE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU 2.9 12.1 + - - +
75A ASN* 3.5 35.6 + - - +
76A ASP 3.4 2.6 - - - -
77A ASN* 1.3 76.7 - - - +
79A ASN* 1.3 61.5 - - - +
81A LEU* 3.4 4.1 + - - +
82A ALA* 2.9 28.8 + - - +
97A LYS* 3.9 38.6 - - + +
100A ILE* 3.5 39.0 - - + -
101A VAL* 3.8 20.9 - - + -
104A LEU* 4.4 6.5 - - + -
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Residues in contact with ASN 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASP 5.3 0.6 + - - -
77A ASN 3.5 0.4 - - - -
78A MSE 1.3 78.4 - - - +
80A GLU* 1.3 62.2 + - - +
82A ALA* 3.5 2.0 + - - +
83A GLU* 3.1 24.9 + - - +
93A ILE* 5.7 0.7 - - - +
97A LYS* 2.9 33.2 + - - +
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Residues in contact with GLU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASN* 3.3 22.8 + - - +
79A ASN* 1.3 77.9 - - - +
81A LEU* 1.3 61.7 + - - +
83A GLU* 3.3 7.7 + - - +
84A MSE 3.2 44.3 + - + +
182A ARG* 3.1 38.7 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A LEU* 3.8 33.2 - - + +
77A ASN* 2.9 39.9 + - + +
78A MSE 3.7 4.0 - - - +
80A GLU* 1.3 72.9 - - - +
82A ALA* 1.3 57.3 + - - +
84A MSE 3.3 10.2 - - - +
85A LEU* 3.0 30.2 + - - +
100A ILE* 4.2 24.0 - - + -
179A VAL* 3.6 12.4 - - + +
182A ARG* 3.8 31.6 - - + -
183A LEU* 4.1 18.6 - - + -
186A LEU* 4.2 3.6 - - + -
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Residues in contact with ALA 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MSE 2.9 17.4 + - - +
79A ASN 3.9 3.4 - - - +
80A GLU 3.3 0.2 - - - -
81A LEU* 1.3 76.3 - - - +
83A GLU* 1.3 58.4 + - - +
85A LEU* 3.3 2.2 + - - +
86A SER* 2.9 34.7 + - - -
93A ILE* 4.1 15.7 - - + +
96A ALA* 3.9 20.2 - - + -
97A LYS* 3.8 28.5 - - + +
100A ILE* 4.8 2.2 - - + +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASN 3.1 18.7 + - - +
80A GLU* 3.3 6.7 + - - +
82A ALA* 1.3 76.8 - - - +
84A MSE 1.3 62.7 + - - +
86A SER* 3.9 1.0 - - - -
87A ARG* 2.8 67.7 + - - +
93A ILE* 3.9 15.1 - - + +
312A TYR* 3.5 23.8 + - + -
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Residues in contact with MSE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A GLU* 3.2 49.3 + - + +
81A LEU* 3.3 14.4 - - - +
83A GLU* 1.3 79.2 + - - +
85A LEU* 1.3 66.7 + - - +
87A ARG* 3.5 24.1 - - - +
88A GLU* 3.4 29.3 + - - +
178A SER* 3.6 38.8 - - - +
179A VAL* 3.5 13.0 - - + -
182A ARG* 3.9 21.3 - - + -
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU 3.0 16.6 + - - +
82A ALA 3.6 4.0 - - - +
84A MSE 1.3 76.5 - - - +
86A SER* 1.3 56.1 + - - +
88A GLU* 3.3 3.5 + - - +
89A HIS* 2.8 45.7 + - + +
91A LYS* 3.5 28.3 - - - -
96A ALA* 3.9 15.0 - - + +
99A ASP* 3.7 24.2 - - - +
100A ILE* 3.9 24.7 - - + -
150A PRO* 3.7 28.3 - - + -
151A GLY 4.5 1.1 - - - +
176A ASP* 5.1 1.8 - - - +
179A VAL* 3.6 12.1 - - + -
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Residues in contact with SER 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA 2.9 21.8 + - - -
83A GLU 4.1 0.4 - - - -
85A LEU* 1.3 74.4 - - - +
87A ARG* 1.3 59.9 + - - +
90A GLY* 2.8 30.4 + - - +
91A LYS 2.9 26.9 + - - +
92A THR 3.1 17.5 + - - -
93A ILE* 3.5 8.6 + - - -
96A ALA* 3.3 6.1 - - - +
312A TYR* 3.6 23.7 - - - -
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A TYR* 3.2 26.6 + - - -
23A ASN* 3.8 15.5 - - - +
24A PRO* 3.6 12.5 - - - +
30A GLN* 3.0 45.9 + - - +
83A GLU* 2.8 45.2 + - - +
84A MSE 3.5 20.8 - - - +
85A LEU 3.3 0.2 - - - -
86A SER* 1.3 77.0 - - - +
88A GLU* 1.3 64.3 + - - +
178A SER* 5.2 2.0 + - - -
312A TYR* 3.5 32.7 - - + +
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Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A TYR* 2.6 31.7 + - - +
21A ILE* 3.6 21.7 - - + +
22A PHE 3.8 4.8 - - - +
24A PRO* 3.4 13.7 - - - +
30A GLN* 3.7 7.0 - - - +
84A MSE 3.4 12.2 + - - +
85A LEU* 3.3 2.6 + - - +
86A SER 3.2 0.2 - - - -
87A ARG* 1.3 81.3 - - - +
89A HIS* 1.3 63.3 + - - +
175A ARG 4.4 5.9 - - - +
176A ASP* 3.2 26.1 - - + +
177A PRO* 4.0 2.2 - - - -
178A SER* 2.6 50.9 + - - -
179A VAL* 4.6 1.2 + - - +
323A VAL* 4.7 6.4 - - - +
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Residues in contact with HIS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.5 9.8 - - - +
85A LEU* 2.8 30.4 + - + +
88A GLU* 1.3 75.3 - - - +
90A GLY* 1.3 56.7 + - - +
91A LYS* 3.1 42.9 + - + +
147A PHE* 3.3 36.1 - + - -
148A ASN* 3.5 28.9 + - - +
150A PRO* 4.6 1.3 - - + -
176A ASP* 3.7 12.8 - - - +
274A SER* 5.1 5.4 - - - -
277A GLU* 3.6 23.6 + - + +
321A PRO 4.4 2.9 - - - +
323A VAL* 3.9 19.4 + - - +
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Residues in contact with GLY 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.6 15.9 - - - +
25A ALA* 5.6 1.1 - - - -
86A SER 2.8 19.6 + - - -
88A GLU 3.6 0.6 - - - -
89A HIS* 1.3 73.8 - - - +
91A LYS* 1.3 64.2 + - - +
312A TYR* 4.6 10.1 + - - +
320A GLY* 3.8 4.7 - - - -
321A PRO* 3.3 34.4 - - - +
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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