Contacts of the helix formed by residues 153 - 158 (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 PHE 153 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C LEU* 4.4 27.6 - - + -
69C ALA* 6.4 0.2 - - + -
70C VAL* 4.1 17.0 - - + -
90C VAL* 4.0 19.3 - - + -
102C LEU* 3.9 22.9 - - + -
106C LEU* 3.6 36.6 - - + -
149C ILE* 2.9 26.2 + - + +
150C ARG 3.1 2.9 - - - -
152C ILE* 1.3 93.0 - - + +
154C LEU* 1.3 65.1 + - - +
155C PHE 3.0 3.6 - - - +
156C LEU* 2.7 29.7 + - + +
157C ASP* 3.1 9.2 + - - +
170C ILE* 3.6 18.8 - - + -
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Residues in contact with LEU 154 (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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585A GLU 5.4 1.3 - - - +
586A ILE* 4.1 29.6 - - + -
587A ILE* 4.3 13.5 - - + -
589A ARG* 5.1 0.2 - - - -
607A GLY* 3.5 36.8 - - - +
635A PRO* 4.6 4.7 - - + -
87C TYR* 3.9 17.9 - - + +
150C ARG* 2.6 32.4 + - + +
151C SER* 3.7 18.4 - - - +
152C ILE 3.2 3.2 + - - -
153C PHE* 1.3 72.5 - - - +
155C PHE* 1.3 58.4 + - - +
157C ASP* 3.2 5.1 + - + +
158C ARG* 2.9 42.2 + - + +
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Residues in contact with PHE 155 (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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634A GLN* 5.0 9.6 - - - -
635A PRO* 3.8 27.6 - - + -
677A ASN* 5.3 9.6 - - - -
87C TYR* 3.9 17.7 - - + -
90C VAL* 4.9 3.4 - - + -
91C GLU* 3.4 63.3 - - + +
94C CYS* 3.6 30.1 - - + -
153C PHE 2.9 1.4 + - - -
154C LEU* 1.3 81.3 - - - +
156C LEU* 1.3 57.9 + - - +
158C ARG 4.2 0.4 - - - +
159C THR* 2.8 57.1 + - + -
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Residues in contact with LEU 156 (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* 4.3 6.6 - - + +
94C CYS* 3.2 29.1 - - - -
99C SER* 3.9 6.3 - - - +
102C LEU* 4.2 15.3 - - + -
103C TYR* 3.9 35.7 - - + +
106C LEU* 5.0 6.3 - - + -
153C PHE* 2.7 34.7 + - + +
155C PHE* 1.3 75.0 - - - +
157C ASP* 1.3 59.4 + - - +
160C TYR* 3.5 29.0 + - + -
161C VAL* 3.2 22.2 + - + +
170C ILE* 5.6 2.0 - - + -
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Residues in contact with ASP 157 (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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150C ARG* 3.6 19.9 + - + +
153C PHE 3.1 5.6 + - - +
154C LEU* 3.8 9.4 - - + +
156C LEU* 1.3 78.9 - - - +
158C ARG* 1.3 64.4 + - + +
159C THR 3.2 0.4 - - - -
161C VAL* 3.6 10.7 - - - +
162C LEU* 2.8 34.8 + - - +
169C SER* 3.6 22.7 + - - -
170C ILE* 2.7 52.6 + - + +
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Residues in contact with ARG 158 (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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586A ILE* 5.2 0.2 - - - +
607A GLY 3.4 25.6 - - - +
608A ASP* 3.1 39.1 + - - +
633A THR* 2.5 49.8 + - - +
634A GLN* 3.4 17.0 - - - +
635A PRO* 4.6 5.4 - - + -
798A THR* 3.8 23.4 - - - +
800A GLU* 5.3 1.6 + - - -
150C ARG* 4.5 15.6 - - - +
154C LEU* 2.9 29.5 + - + +
155C PHE 4.1 0.9 - - - -
157C ASP* 1.3 80.4 - - + +
159C THR* 1.3 59.8 + - - +
162C LEU* 2.9 38.1 - - + +
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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