Contacts of the helix formed by residues 77 - 90 (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 ASN 77 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73B LEU* 2.8 33.7 + - - +
74B LEU 3.5 3.6 - - - +
76B ASP* 1.3 85.6 - - - +
78B MSE 1.3 63.8 + - - +
79B ASN 3.4 2.5 - - - -
80B GLU* 3.3 20.9 + - - +
81B LEU* 3.0 33.7 + - + +
182B ARG* 3.3 19.2 + - - +
186B LEU* 3.6 25.3 - - + +
189B GLU* 5.4 0.6 + - - -
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Residues in contact with MSE 78 (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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74B LEU 3.0 23.1 + - - +
75B ASN* 3.3 31.7 + - - +
76B ASP 3.4 1.2 - - - -
77B ASN* 1.3 76.7 - - - +
79B ASN* 1.3 61.3 + - - +
81B LEU* 3.8 3.9 - - - +
82B ALA* 2.9 31.8 + - - +
97B LYS* 4.0 38.6 - - + +
100B ILE* 3.8 34.1 - - + -
101B VAL* 3.7 23.3 - - + -
104B LEU* 4.4 5.4 - - + -
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Residues in contact with ASN 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ASP 5.3 0.2 + - - -
77B ASN 3.4 0.8 - - - -
78B MSE 1.3 80.3 - - - +
80B GLU* 1.3 57.2 + - - +
82B ALA* 3.5 5.4 + - - +
83B GLU* 3.0 29.2 + - - +
93B ILE* 5.4 0.5 - - - +
97B LYS* 3.1 30.5 - - - +
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Residues in contact with GLU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASN* 3.3 27.8 + - - +
79B ASN* 1.3 79.4 - - - +
81B LEU* 1.3 63.0 + - - +
83B GLU* 3.3 7.5 + - - +
84B MSE 3.2 41.5 + - + +
182B ARG* 3.0 35.2 + - - +
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Residues in contact with LEU 81 (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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74B LEU* 4.0 35.7 - - + +
77B ASN* 3.0 24.6 + - + +
78B MSE 3.8 3.8 - - - +
80B GLU* 1.3 73.7 - - - +
82B ALA* 1.3 64.7 + - - +
84B MSE 3.4 8.5 - - - +
85B LEU* 3.1 25.5 + - - +
100B ILE* 4.2 26.9 - - + -
179B VAL* 3.6 17.6 - - + +
182B ARG* 3.7 32.8 - - + -
183B LEU* 4.2 16.8 - - + -
186B LEU* 4.3 9.0 - - + -
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Residues in contact with ALA 82 (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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78B MSE 2.9 17.7 + - - +
79B ASN* 3.7 4.3 - - - +
81B LEU* 1.3 76.8 - - - +
83B GLU* 1.3 55.9 + - - +
85B LEU* 3.4 0.6 + - - -
86B SER* 3.0 35.5 + - - -
93B ILE* 3.7 13.5 - - + +
96B ALA* 3.6 20.7 - - + +
97B LYS* 3.8 31.4 - - + +
100B ILE* 4.8 2.1 - - - +
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Residues in contact with GLU 83 (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 ASN 3.0 17.4 + - - +
80B GLU* 3.6 8.4 - - - +
81B LEU 3.3 0.2 - - - -
82B ALA* 1.3 77.3 - - - +
84B MSE 1.3 61.8 + - - +
86B SER* 3.9 1.7 - - - -
87B ARG* 3.0 64.9 + - - +
93B ILE* 3.8 11.8 - - + +
312B TYR* 3.4 24.0 + - + -
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Residues in contact with MSE 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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80B GLU* 3.2 44.9 + - + +
81B LEU* 3.4 13.0 - - - +
83B GLU* 1.3 78.4 + - - +
85B LEU* 1.3 70.5 + - - +
87B ARG* 3.6 25.9 + - - +
88B GLU* 3.4 28.5 + - - +
178B SER* 3.8 35.4 - - - +
179B VAL* 3.5 13.2 - - + -
182B ARG* 3.9 22.7 - - + -
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Residues in contact with LEU 85 (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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81B LEU 3.1 15.8 + - - +
82B ALA 3.6 4.5 - - - +
84B MSE 1.3 80.3 - - - +
86B SER* 1.3 58.8 + - - +
88B GLU* 3.8 3.6 - - - +
89B HIS* 2.8 41.8 + - + +
91B LYS* 3.5 28.5 - - + -
96B ALA* 3.9 14.1 - - + +
99B ASP* 3.5 28.5 - - - +
100B ILE* 3.8 25.1 - - + -
150B PRO* 4.0 19.7 - - + -
151B GLY 4.5 1.6 - - - +
176B ASP* 5.1 1.2 - - - +
179B VAL* 3.7 14.8 - - + -
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Residues in contact with SER 86 (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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82B ALA 3.0 17.4 + - - -
83B GLU 4.0 0.2 - - - -
85B LEU* 1.3 76.9 - - - +
87B ARG* 1.3 59.1 + - - +
89B HIS* 4.7 0.9 - - - -
90B GLY* 2.8 32.2 + - - +
91B LYS 2.9 27.1 + - - +
92B THR 3.4 4.5 + - - -
93B ILE* 3.5 11.5 - - - +
96B ALA* 3.3 14.4 - - - +
312B TYR* 3.5 25.2 - - - -
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Residues in contact with ARG 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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0B TYR* 3.2 28.3 + - - -
23B ASN* 3.5 13.7 - - - +
24B PRO* 3.4 15.2 - - - +
30B GLN* 2.9 47.4 + - - +
83B GLU* 3.0 46.4 + - - +
84B MSE 3.6 23.0 - - - +
85B LEU 3.2 0.4 - - - -
86B SER* 1.3 76.4 - - - +
88B GLU* 1.3 61.2 + - - +
178B SER* 5.3 2.0 + - - -
312B TYR* 3.5 32.5 - - + +
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Residues in contact with GLU 88 (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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0B TYR* 2.8 29.0 + - - +
21B ILE* 3.7 8.9 - - + +
22B PHE 3.7 4.7 - - - +
24B PRO* 3.4 13.3 - - - +
30B GLN* 3.8 10.5 - - - +
84B MSE 3.4 12.1 + - - +
85B LEU* 3.2 3.1 + - - +
87B ARG* 1.3 81.0 - - - +
89B HIS* 1.3 62.2 + - - +
175B ARG 4.3 8.8 - - - +
176B ASP* 3.2 27.1 - - + +
177B PRO* 3.9 10.3 - - - +
178B SER* 2.6 52.4 + - - -
179B VAL 4.5 0.9 + - - -
323B VAL* 4.6 7.4 - - - +
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Residues in contact with HIS 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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24B PRO* 3.5 9.1 - - - +
85B LEU* 2.8 25.8 + - + +
88B GLU* 1.3 78.5 - - - +
90B GLY* 1.3 56.5 + - - +
91B LYS* 3.3 39.3 + - + +
147B PHE* 3.3 33.5 - + - -
148B ASN* 3.3 31.6 + - - +
150B PRO* 4.5 1.8 - - + -
176B ASP* 3.7 12.1 - - - +
274B SER* 5.2 4.5 - - - -
277B GLU* 3.5 28.0 + - + -
321B PRO 4.5 1.9 - - - +
323B VAL* 3.9 22.1 + - - +
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Residues in contact with GLY 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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24B PRO* 3.5 15.9 - - - +
25B ALA* 6.1 0.9 - - - -
86B SER 2.8 19.1 + - - -
89B HIS* 1.3 74.4 - - - +
91B LYS* 1.3 65.6 + - - +
92B THR 3.9 0.2 + - - -
312B TYR* 4.5 11.5 + - - -
320B GLY* 3.9 4.6 - - - -
321B PRO* 3.4 34.1 - - - +
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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