Contacts of the helix formed by residues 136 - 145 (chain C) in PDB entry 5F1B
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 136 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C TYR* 3.3 24.1 + - - -
125C HIS 3.5 18.2 - - - +
126C LYS* 4.4 9.0 - - + +
133C VAL* 4.1 9.4 - - + +
135C ALA* 1.3 75.0 - - - +
137C TYR* 1.3 69.1 + - + +
138C HIS* 2.7 45.0 + - - +
139C THR* 3.1 8.4 + - - +
140C HIS* 3.0 23.0 + - - +
157C LEU* 4.0 4.8 - - - +
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Residues in contact with TYR 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 3.7 6.8 + - - -
59C PHE* 5.4 2.9 - + - -
63C LEU* 2.8 31.7 + - + -
65C ILE* 3.4 42.0 + - + +
68C LEU* 3.7 21.3 - - + -
116C PHE* 3.5 29.1 - + + -
122C VAL 5.9 0.4 - - - -
123C LEU* 3.4 22.2 + - + +
125C HIS 4.2 3.2 + - - -
136C ASP* 1.3 79.4 - - + +
138C HIS* 1.3 103.3 + + - +
140C HIS* 4.2 0.2 - - - -
141C PHE* 2.8 38.6 + - + +
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Residues in contact with HIS 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C HIS* 2.9 27.1 + + - -
48C TYR* 3.5 42.8 - + + +
59C PHE* 3.6 39.4 - + + -
136C ASP* 2.7 27.6 + - - +
137C TYR* 1.3 110.9 + + - +
139C THR* 1.3 58.5 + - + +
141C PHE* 3.2 4.7 + - - +
142C LEU* 2.9 33.2 + - + +
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Residues in contact with THR 139 (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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48C TYR* 4.4 5.2 - - + +
50C PRO* 3.5 35.0 - - + -
51C TYR 4.7 5.6 - - - +
134C TYR 4.7 6.1 - - - +
135C ALA* 3.5 16.1 - - - +
136C ASP* 3.1 30.3 + - - +
138C HIS* 1.3 77.4 - - - +
140C HIS* 1.3 66.6 + - - +
142C LEU* 3.9 7.6 - - - +
143C TYR* 3.1 25.6 + - - +
153C ASP* 5.3 0.8 + - - -
155C SER* 4.9 7.2 - - - -
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Residues in contact with HIS 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 2.7 32.0 + - + -
116C PHE* 3.7 27.6 - + + -
117C GLN* 5.4 0.4 + - - -
122C VAL* 5.6 0.6 - - + +
136C ASP 3.0 17.9 + - - +
137C TYR* 3.7 4.0 - - - +
139C THR* 1.3 78.9 + - - +
141C PHE* 1.3 55.9 + - - +
143C TYR* 3.8 2.0 - - - +
144C CYS* 2.8 57.0 + - - -
153C ASP* 2.6 29.6 + - + +
157C LEU* 6.2 2.0 - - + -
159C ASP* 3.3 29.6 - - + +
160C PRO 2.9 20.4 + - - -
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Residues in contact with PHE 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C PHE* 3.8 17.3 - + + -
63C LEU* 3.7 25.8 - - + -
112C VAL* 3.7 31.2 - - + -
115C TYR* 4.7 4.7 - + - -
116C PHE* 4.5 9.2 - + + -
137C TYR* 2.8 25.9 + - + +
138C HIS* 3.2 5.8 + - - +
140C HIS* 1.3 74.6 - - - +
142C LEU* 1.3 72.7 + - + +
144C CYS* 3.2 4.2 + - - +
145C VAL* 3.1 50.4 + - + +
175C LEU* 3.8 11.7 - - + -
183C TYR* 3.8 13.0 - - + -
184C ASN* 3.6 27.6 - - + -
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Residues in contact with LEU 142 (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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50C PRO* 4.3 25.1 - - + -
57C VAL* 4.2 16.8 - - + -
59C PHE* 3.8 17.7 - - + -
138C HIS* 2.9 26.7 + - + +
139C THR* 3.4 5.6 + - - +
141C PHE* 1.3 79.8 - - + +
143C TYR* 1.3 62.5 + - - +
145C VAL* 3.3 18.6 - - + +
146C ARG* 3.8 14.9 - - - +
184C ASN* 4.0 33.7 - - + +
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Residues in contact with TYR 143 (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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139C THR 3.1 17.5 + - - +
140C HIS 3.9 1.6 - - - +
142C LEU* 1.3 77.0 - - - +
144C CYS* 1.3 61.4 + - - +
146C ARG* 3.0 25.0 + - + +
147C ALA* 3.1 26.5 + - + +
150C SER* 2.9 38.1 + - - -
152C ASN 3.3 9.2 + - - -
153C ASP* 3.4 44.0 - - + +
154C THR* 3.9 17.5 - - + +
161C CYS* 3.6 8.1 - - - -
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Residues in contact with CYS 144 (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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115C TYR* 3.7 28.2 - - + -
140C HIS* 2.8 55.2 + - - +
141C PHE 3.9 2.0 - - - +
143C TYR* 1.3 73.9 - - - +
145C VAL* 1.3 58.5 + - - +
147C ALA 3.8 0.7 - - - -
148C PRO* 3.1 33.1 - - - +
161C CYS* 2.0 50.5 - - - -
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Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C TYR* 3.9 14.6 - - + -
141C PHE* 3.1 44.1 + - + +
142C LEU* 3.3 25.1 - - + +
144C CYS* 1.3 75.7 - - - +
146C ARG* 1.3 64.0 + - + +
148C PRO* 4.0 2.8 - - - +
171C PRO* 3.2 40.5 - - + +
175C LEU* 4.6 0.7 - - + -
183C TYR* 3.7 33.0 - - + -
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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