Contacts of the helix formed by residues 82 - 94 (chain C) in PDB entry 2HYE
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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499A SER* 4.3 1.4 + - - -
513A GLY* 3.7 21.0 + - - +
514A ARG* 5.7 0.9 - - - +
537A GLU* 3.1 30.0 - - - +
79C ILE* 4.9 7.0 + - - +
80C ARG* 3.5 5.0 + - - +
81C TYR* 1.3 97.6 + - - +
83C LEU* 1.3 63.0 + - - +
84C GLU* 3.2 3.6 + - - +
85C GLU* 3.5 29.2 + - - +
86C LEU* 5.0 1.4 - - - +
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Residues in contact with LEU 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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537A GLU* 3.3 20.3 + - + +
561A TRP* 3.6 35.9 - - + -
562A THR* 4.6 13.7 - - - +
79C ILE* 5.2 12.7 - - + +
82C ASN* 1.3 66.0 - - - +
84C GLU* 1.2 58.7 + - - +
85C GLU 3.4 0.2 - - - -
86C LEU* 3.1 15.0 + - + +
87C TYR* 2.8 26.5 + - - +
148C MET* 3.9 30.5 - - + -
152C ILE* 3.7 32.8 - - + +
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Residues in contact with GLU 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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499A SER* 3.9 21.5 - - - -
500A VAL* 4.0 10.5 - - - +
513A GLY* 6.5 0.4 - - - -
537A GLU* 3.9 8.9 + - + +
538A VAL 2.9 24.6 - - - +
539A ALA* 3.1 6.8 - - - -
561A TRP* 3.1 27.9 + - + +
589A ARG* 2.7 24.3 + - - -
82C ASN* 3.2 5.0 + - - +
83C LEU* 1.2 72.1 - - - +
85C GLU* 1.3 60.9 + - - +
87C TYR* 3.1 3.0 + - - +
88C GLN* 2.6 62.5 + - - +
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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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497A ASN* 3.9 28.4 + - - +
498A ILE 4.7 2.5 - - - +
499A SER* 3.8 26.5 + - - +
65C LYS* 5.1 16.4 + - - +
81C TYR* 3.5 19.9 - - + +
82C ASN* 3.5 22.7 + - - +
83C LEU 3.4 0.6 - - - -
84C GLU* 1.3 75.6 - - - +
86C LEU* 1.3 58.9 + - - +
88C GLN* 3.3 9.5 + - - +
89C ALA* 2.8 29.1 + - - +
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Residues in contact with LEU 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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65C LYS* 3.3 40.4 - - + +
66C LEU* 3.4 21.0 - - + +
69C ALA* 3.4 23.1 - - + -
79C ILE* 5.4 7.0 - - + -
81C TYR* 3.8 25.8 - - + +
82C ASN 4.2 0.8 + - - +
83C LEU* 3.1 20.9 + - + +
85C GLU* 1.3 78.2 - - - +
87C TYR* 1.3 59.0 + - - +
89C ALA* 3.2 14.4 - - + +
90C VAL* 2.9 22.3 - - - +
152C ILE* 3.8 24.2 - - + -
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Residues in contact with TYR 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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561A TRP* 3.9 15.3 - + + -
587A ILE* 5.7 1.8 - - + -
589A ARG* 2.9 60.7 - - - +
635A PRO* 3.7 18.0 - - - +
83C LEU 2.8 13.4 + - - +
84C GLU* 3.1 11.4 + - - +
86C LEU* 1.3 75.3 - - - +
88C GLN* 1.3 67.3 - - + +
90C VAL* 3.0 20.1 + - - +
91C GLU* 3.0 33.7 + - - +
151C SER 4.1 7.9 - - - -
152C ILE* 3.5 24.6 - - - +
154C LEU* 3.9 11.8 - - + +
155C PHE* 3.9 26.0 - - + -
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Residues in contact with GLN 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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458A PHE* 4.1 18.5 - - - -
498A ILE 5.4 0.3 - - - +
499A SER* 3.2 22.0 + - - +
589A ARG* 5.3 2.2 - - - +
84C GLU* 2.6 59.0 + - - +
85C GLU* 3.8 7.3 - - - +
87C TYR* 1.3 79.9 - - + +
89C ALA* 1.3 66.1 + - - +
91C GLU* 4.3 8.1 - - + +
92C ASN* 2.9 37.3 + - - +
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Residues in contact with ALA 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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62C THR* 4.0 25.3 - - + +
65C LYS* 5.1 10.3 - - - +
66C LEU* 5.1 6.3 - - + -
85C GLU 2.8 14.3 + - - +
86C LEU* 3.2 17.0 - - + +
87C TYR 3.1 0.2 - - - -
88C GLN* 1.3 78.0 - - - +
90C VAL* 1.3 58.0 + - + +
92C ASN* 4.2 2.3 - - - +
93C LEU* 2.9 32.5 + - - +
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Residues in contact with VAL 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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66C LEU* 4.8 11.0 - - + -
86C LEU 2.9 19.1 - - - +
87C TYR 3.0 8.0 + - - +
89C ALA* 1.3 72.5 - - - +
91C GLU* 1.3 51.0 + - - +
92C ASN 2.5 12.3 + - - -
93C LEU* 2.6 5.1 + - - -
94C CYS* 2.4 42.2 + - + -
102C LEU* 3.9 25.4 - - + -
152C ILE* 3.6 26.9 - - + +
153C PHE* 4.0 19.3 - - + -
155C PHE* 4.9 3.8 - - + -
156C LEU* 4.3 12.1 - - + +
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Residues in contact with GLU 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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408A LYS* 3.7 11.1 + - - -
589A ARG* 4.6 3.9 + - - +
635A PRO* 5.0 1.7 - - - +
678A TYR* 3.3 24.5 + - - +
87C TYR* 3.0 37.3 + - + +
88C GLN* 3.9 13.7 - - - +
90C VAL* 1.3 77.1 - - - +
92C ASN* 1.3 63.8 + - - +
94C CYS* 3.8 11.8 - - - +
95C SER* 5.8 0.2 - - - -
155C PHE* 3.4 45.7 - - + +
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Residues in contact with ASN 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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408A LYS* 2.6 49.6 + - - +
430A VAL* 4.3 27.7 - - + +
456A GLN* 3.8 21.5 + - - +
88C GLN* 2.9 31.2 + - - +
89C ALA* 4.2 2.7 - - - +
90C VAL 2.5 5.3 + - - -
91C GLU* 1.3 80.3 - - - +
93C LEU* 1.3 65.7 + - - +
94C CYS 3.1 4.7 + - - -
95C SER* 4.2 7.6 + - - -
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Residues in contact with LEU 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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59C THR* 5.7 7.2 - - + -
62C THR* 3.9 19.7 - - + -
63C TRP* 3.3 47.1 - - + +
66C LEU* 4.5 12.6 - - + -
89C ALA 2.9 20.8 + - - +
90C VAL* 2.6 7.4 + - - +
92C ASN* 1.3 74.9 - - - +
94C CYS* 1.3 54.8 + - - +
95C SER* 2.9 11.3 + - - -
98C VAL* 3.7 29.1 - - + +
102C LEU* 4.5 10.9 - - + +
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Residues in contact with CYS 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 VAL* 2.4 43.4 + - + +
91C GLU 3.8 3.7 - - - +
92C ASN 3.1 2.2 - - - -
93C LEU* 1.3 63.0 - - - +
95C SER* 1.3 58.6 + - - +
98C VAL 5.8 0.2 - - - -
99C SER* 3.3 20.4 + - - +
102C LEU* 4.5 5.8 - - - +
155C PHE* 3.6 28.6 - - + -
156C LEU* 3.2 49.1 - - - -
159C THR* 5.2 6.5 - - - +
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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