Contacts of the helix formed by residues 79 - 97 (chain C) in PDB entry 4YCV
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 ASP 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78C VAL* 1.3 77.5 - - - +
80C PRO* 1.3 74.9 - - + +
82C LEU* 4.0 36.8 - - + +
83C TYR* 3.5 17.0 + - - +
220C MET* 4.6 0.9 - - - +
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Residues in contact with PRO 80 (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 VAL 3.6 2.8 - - - +
79C ASP* 1.3 86.0 - - + +
81C ARG* 1.3 75.1 + - + +
83C TYR* 2.9 15.6 + - + +
84C PHE* 3.0 12.7 + - - +
220C MET* 4.1 22.6 + - + +
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Residues in contact with ARG 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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79C ASP* 3.6 0.6 - - - +
80C PRO* 1.3 83.3 - - + +
82C LEU* 1.3 67.3 + - + +
84C PHE* 3.0 13.8 + - - +
85C GLU* 2.9 44.0 + - - +
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Residues in contact with LEU 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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79C ASP* 4.0 26.9 - - + +
81C ARG* 1.3 85.9 - - + +
83C TYR* 1.3 60.0 + - - +
85C GLU* 4.0 13.6 - - - +
86C ASN* 2.9 44.8 + - - +
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Residues in contact with TYR 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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78C VAL* 5.6 6.7 - - + -
79C ASP 3.5 14.2 + - - +
80C PRO* 2.9 13.4 + - + +
82C LEU* 1.3 78.1 - - - +
84C PHE* 1.3 57.5 - - - +
86C ASN* 3.6 7.3 - - - +
87C ARG* 3.0 43.6 + - + +
185C ARG* 3.6 53.1 - - - +
186C ARG* 4.4 11.3 + - - +
217C CYS 4.8 2.2 + - - -
218C LEU 3.4 21.3 - - - -
219C HIS 3.8 4.9 - - - -
220C MET* 3.7 43.6 - - + -
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Residues in contact with PHE 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 PRO 3.0 8.1 + - - +
81C ARG* 3.0 14.1 + - - +
83C TYR* 1.3 79.4 - - - +
85C GLU* 1.3 64.0 + - + +
87C ARG* 3.2 2.6 + - - +
88C SER* 2.9 43.5 + - - -
218C LEU* 3.4 50.5 - - + +
219C HIS* 3.9 33.2 - + + +
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Residues in contact with GLU 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 ARG* 2.9 33.6 + - - +
82C LEU* 4.0 10.6 - - - +
84C PHE* 1.3 78.9 - - + +
86C ASN* 1.3 62.1 + - - +
88C SER* 3.6 8.1 - - - -
89C LYS* 2.9 30.9 + - - +
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Residues in contact with ASN 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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82C LEU* 2.9 31.9 + - - +
83C TYR* 3.6 8.2 - - - +
85C GLU* 1.3 79.2 - - - +
87C ARG* 1.3 57.4 + - + +
89C LYS* 3.5 7.0 + - - +
90C PHE* 2.9 25.5 + - - +
185C ARG* 6.0 4.3 - - - +
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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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83C TYR* 3.0 31.3 + - + +
84C PHE 3.6 4.7 - - - +
86C ASN* 1.3 76.3 - - + +
88C SER* 1.3 59.7 + - - +
90C PHE* 3.1 29.2 + - - +
91C ILE* 2.9 36.3 + - - +
183C LYS 3.3 23.4 + - - -
185C ARG* 3.3 35.2 - - - +
188C ASP* 2.6 39.3 + - - -
216C ALA* 3.6 16.1 - - - +
217C CYS 3.3 16.0 + - - -
218C LEU* 3.6 26.0 - - + +
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Residues in contact with SER 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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84C PHE* 2.9 41.3 + - - -
85C GLU* 3.6 8.7 - - - -
87C ARG* 1.3 75.4 - - - +
89C LYS* 1.3 57.7 + - - +
91C ILE* 3.2 9.2 + - - +
92C GLN* 3.0 28.7 + - - +
218C LEU* 4.4 9.5 - - - +
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Residues in contact with LYS 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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85C GLU 2.9 18.6 + - - +
86C ASN* 3.7 7.9 - - - +
88C SER* 1.3 73.7 - - - +
90C PHE* 1.3 61.2 + - - +
92C GLN* 3.8 6.8 - - - +
93C ASP* 2.9 38.5 + - - +
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Residues in contact with PHE 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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86C ASN 2.9 15.8 + - - +
87C ARG* 3.1 38.1 + - - +
89C LYS* 1.3 73.5 - - - +
91C ILE* 1.3 90.0 + - + +
93C ASP* 3.2 7.2 + - + +
94C GLN* 2.9 57.0 + - + +
101C PRO* 5.4 0.7 - - + -
183C LYS* 3.8 32.1 - - + -
213C LEU* 4.7 11.2 - - + -
216C ALA* 5.5 0.9 - - + -
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Residues in contact with ILE 91 (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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87C ARG* 2.9 19.4 + - + +
88C SER* 3.2 8.9 + - - +
90C PHE* 1.3 96.7 - - + +
92C GLN* 1.3 58.4 + - - +
94C GLN* 3.3 3.2 + - - +
95C LYS* 2.9 41.5 + - - +
101C PRO* 3.7 30.2 - - + +
102C TYR* 4.0 17.9 - - + +
216C ALA* 3.7 25.1 - - + -
218C LEU* 4.4 15.3 - - + -
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Residues in contact with GLN 92 (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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88C SER 3.0 16.5 + - - +
89C LYS* 3.9 7.0 - - - +
91C ILE* 1.3 76.3 - - - +
93C ASP* 1.3 61.2 + - - +
95C LYS* 3.2 29.7 + - - +
96C ASP* 2.9 51.3 + - - +
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Residues in contact with ASP 93 (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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89C LYS* 2.9 24.6 + - - +
90C PHE* 3.2 7.9 + - + +
92C GLN* 1.3 80.9 - - - +
94C GLN* 1.3 57.7 + - + +
96C ASP* 3.2 13.6 + - - +
97C LYS* 2.9 24.9 + - - +
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Residues in contact with GLN 94 (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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90C PHE* 2.9 47.2 + - + +
91C ILE 4.0 3.1 - - - +
93C ASP* 1.3 74.6 - - + +
95C LYS* 1.3 58.9 + - - +
96C ASP 3.2 0.2 - - - -
97C LYS* 3.3 4.3 + - + +
98C GLY 3.3 2.8 + - - -
99C ILE* 2.6 81.8 + - + +
101C PRO* 4.3 15.3 - - + +
180C CYS* 6.2 2.2 - - - -
183C LYS* 4.9 7.1 - - - +
213C LEU* 4.9 6.7 - - - +
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Residues in contact with LYS 95 (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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91C ILE* 2.9 29.2 + - + +
92C GLN* 3.4 32.9 + - - +
94C GLN* 1.3 76.0 - - - +
96C ASP* 1.3 61.7 + - - +
98C GLY* 2.9 20.4 + - - -
99C ILE 3.5 6.5 + - - +
100C ASN* 5.7 0.9 - - - +
101C PRO* 4.2 14.6 - - + +
102C TYR* 6.1 3.6 - - - -
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Residues in contact with ASP 96 (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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92C GLN* 2.9 38.4 + - - +
93C ASP* 3.4 16.7 - - - +
94C GLN 3.2 0.2 - - - -
95C LYS* 1.3 74.7 - - - +
97C LYS* 1.3 59.4 + - - +
98C GLY* 3.0 5.8 + - - -
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Residues in contact with LYS 97 (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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93C ASP 2.9 15.2 + - - +
94C GLN* 3.7 4.5 - - + +
95C LYS 3.2 0.4 - - - -
96C ASP* 1.3 76.0 - - - +
98C GLY* 1.3 55.9 + - - +
99C ILE* 3.2 32.6 + - + +
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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