Contacts of the helix formed by residues 77 - 90 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73C LEU* 2.9 31.7 + - - +
74C LEU 3.4 3.1 - - - +
76C ASP* 1.3 86.1 - - - +
78C MSE 1.3 65.5 + - - +
80C GLU* 3.1 24.8 - - + +
81C LEU* 2.9 36.1 + - + +
182C ARG* 2.9 30.0 + - - +
186C LEU* 3.9 17.9 - - + +
189C GLU* 5.4 0.8 + - - -
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Residues in contact with MSE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU 2.9 13.6 + - - +
75C ASN* 3.4 36.3 + - - +
76C ASP 3.5 1.0 + - - -
77C ASN* 1.3 75.7 - - - +
79C ASN* 1.3 67.1 + - - +
81C LEU* 3.4 3.7 + - - +
82C ALA* 2.9 23.7 + - - +
97C LYS* 3.9 34.3 - - + +
100C ILE* 3.8 43.7 - - + -
101C VAL* 3.7 24.7 - - + -
104C LEU* 4.3 7.6 - - + -
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Residues in contact with ASN 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76C ASP 5.3 0.2 + - - -
77C ASN 3.3 0.6 - - - -
78C MSE 1.3 81.2 - - - +
80C GLU* 1.3 66.7 + - - +
82C ALA* 3.8 1.9 - - - +
83C GLU* 3.0 29.9 + - - +
93C ILE* 5.3 0.9 - - - +
97C LYS* 2.9 33.8 + - - +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASP 3.9 5.0 - - - +
77C ASN* 3.1 37.0 - - + +
79C ASN* 1.3 78.6 + - - +
81C LEU* 1.3 66.1 + - + +
83C GLU* 3.3 8.6 + - - +
84C MSE 3.1 37.8 + - + +
182C ARG* 5.9 2.7 - - - +
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Residues in contact with LEU 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74C LEU* 3.8 38.8 - - + +
77C ASN* 2.9 30.7 + - + +
78C MSE 3.7 0.9 - - - +
80C GLU* 1.3 77.6 - - + +
82C ALA* 1.3 62.5 + - - +
84C MSE 3.2 12.3 - - + +
85C LEU* 3.1 24.1 + - - +
100C ILE* 3.6 26.7 - - + -
179C VAL* 3.7 12.8 - - + +
182C ARG* 3.8 32.1 - - + -
183C LEU* 4.2 18.6 - - + -
186C LEU* 4.3 3.8 - - + -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C MSE 2.9 16.8 + - - +
79C ASN 3.8 3.8 - - - +
81C LEU* 1.3 75.4 - - - +
83C GLU* 1.3 58.7 + - - +
85C LEU 3.4 0.5 + - - -
86C SER* 2.9 35.0 + - - -
93C ILE* 3.9 16.6 - - + +
96C ALA* 3.6 19.2 - - + +
97C LYS* 3.7 27.1 - - + -
100C ILE* 3.5 6.2 - - + +
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Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C ASN 3.0 18.3 + - - +
80C GLU* 3.3 8.3 + - - +
82C ALA* 1.3 76.1 - - - +
84C MSE 1.3 60.4 + - - +
86C SER* 3.6 1.2 + - - -
87C ARG* 3.0 62.8 + - - +
93C ILE* 3.8 14.1 - - + +
312C TYR* 3.6 23.6 + - + -
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Residues in contact with MSE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C GLU* 3.1 26.3 + - + +
81C LEU* 3.2 18.6 - - + +
83C GLU* 1.3 79.3 + - - +
85C LEU* 1.3 66.3 + - - +
87C ARG* 3.5 21.0 + - - +
88C GLU* 3.3 29.3 + - - +
178C SER* 3.9 28.9 - - - +
179C VAL* 3.8 11.0 - - + -
182C ARG* 3.9 43.7 - - + +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C LEU 3.1 15.4 + - - +
82C ALA 3.6 3.8 - - - +
84C MSE 1.3 77.1 - - - +
86C SER* 1.3 53.7 + - - +
88C GLU* 3.1 7.0 + - - +
89C HIS* 2.8 44.4 + - + +
91C LYS* 3.5 29.4 - - + -
96C ALA* 4.1 17.5 - - + +
99C ASP* 3.6 26.2 - - - +
100C ILE* 4.3 11.4 - - + -
150C PRO* 3.8 23.8 - - + -
151C GLY 4.4 3.1 - - - +
176C ASP* 5.1 1.7 - - - +
179C VAL* 3.6 22.2 - - + -
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Residues in contact with SER 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C ASN* 5.6 0.2 - - - +
24C PRO* 5.0 0.3 - - - +
82C ALA 2.9 21.5 + - - -
83C GLU 4.0 1.3 - - - -
85C LEU* 1.3 74.6 - - - +
87C ARG* 1.3 59.4 + - - +
90C GLY* 2.9 32.0 + - - +
91C LYS* 2.9 25.8 + - - +
92C THR 3.3 16.1 + - - -
93C ILE* 3.5 8.8 + - - -
96C ALA* 3.4 6.9 - - - +
312C TYR* 3.5 25.7 - - - -
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Residues in contact with ARG 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C TYR* 3.2 27.0 + - - -
23C ASN* 3.7 13.1 - - - +
24C PRO* 3.5 13.5 - - - +
30C GLN* 2.8 53.3 + - - +
83C GLU* 3.0 44.7 + - - +
84C MSE 3.6 20.8 - - - +
85C LEU 3.3 0.2 - - - -
86C SER* 1.3 76.4 - - - +
88C GLU* 1.3 63.4 + - - +
178C SER* 5.3 2.0 + - - -
312C TYR* 3.4 36.7 - - + +
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Residues in contact with GLU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C TYR* 2.6 29.4 + - - +
21C ILE* 3.6 8.5 - - + +
22C PHE* 3.7 4.7 - - - +
24C PRO* 3.4 13.3 - - - +
30C GLN* 3.7 9.9 - - - +
84C MSE 3.3 12.3 + - - +
85C LEU* 3.1 4.1 + - - +
87C ARG* 1.3 82.0 - - - +
89C HIS* 1.3 62.2 + - - +
90C GLY 3.7 0.2 - - - -
175C ARG 4.3 9.0 - - - +
176C ASP* 3.1 26.9 - - + +
177C PRO* 3.8 9.6 - - - +
178C SER* 2.6 52.7 + - - -
179C VAL* 4.5 0.9 + - - +
323C VAL* 4.5 7.8 - - - +
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Residues in contact with HIS 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PRO* 3.6 8.8 - - - +
85C LEU* 2.8 25.6 + - + +
88C GLU* 1.3 79.5 - - - +
90C GLY* 1.3 55.3 + - - +
91C LYS* 3.1 40.7 + - + +
147C PHE* 3.3 35.7 - + - -
148C ASN* 3.3 30.0 + - - +
150C PRO* 4.6 1.3 - - + -
176C ASP* 3.7 12.8 - - - +
274C SER* 5.1 4.7 - - - -
277C GLU* 3.5 25.7 + - + +
321C PRO 4.4 2.8 - - - +
323C VAL* 3.9 21.1 + - - +
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Residues in contact with GLY 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PRO* 3.6 16.5 - - - +
25C ALA* 6.4 0.2 - - - -
86C SER 2.9 14.6 + - - +
89C HIS* 1.3 78.6 - - - +
91C LYS* 1.3 65.5 + - - +
311C PRO 5.2 0.2 - - - -
312C TYR* 4.5 10.5 + - - +
320C GLY* 3.9 5.0 - - - -
321C PRO* 3.6 32.3 - - - +
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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