Contacts of the helix formed by residues 151 - 160 (chain A) in PDB entry 5XFR
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 CYS 151 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.3 6.4 - - - -
125A CYS* 4.0 2.7 - - - -
129A TYR* 3.5 35.4 - - + -
134A HIS* 3.6 13.5 - - + -
149A TRP* 3.7 7.9 - - + -
150A LEU* 1.3 75.7 - - - +
152A ARG* 1.3 56.3 + - - +
153A GLN* 3.7 14.6 - - - -
154A CYS 3.0 13.5 + - - -
155A VAL* 2.8 33.0 + - - +
178A MET* 4.4 0.2 - - - -
402A ZN 2.4 34.5 - - - -
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Residues in contact with ARG 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134A HIS* 3.0 28.6 + - + +
135A THR* 3.3 29.0 + - - +
136A PRO* 4.0 1.2 - - - +
151A CYS* 1.3 70.3 - - - +
153A GLN* 1.3 63.2 - - - +
155A VAL* 3.3 0.8 + - - +
156A PHE* 3.0 58.2 + - + -
178A MET* 2.7 47.6 + - - +
179A LYS* 4.1 3.4 - - - +
181A THR 2.9 22.0 + - - -
183A PRO* 3.4 21.6 - - - +
205A TYR 3.2 25.7 + - - -
206A CYS* 6.0 0.2 - - - +
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Residues in contact with GLN 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 6.1 2.4 - - + -
94A GLN* 3.0 48.4 + - - +
125A CYS* 4.3 8.1 - - - +
127A GLN* 4.0 20.2 + - - +
129A TYR* 4.6 5.6 + - - +
151A CYS* 3.2 16.0 - - - -
152A ARG* 1.3 80.4 - - - +
154A CYS* 1.3 60.5 + - - +
156A PHE* 3.6 5.3 + - - +
157A ALA* 3.2 25.1 + - + +
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Residues in contact with CYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A CYS* 3.7 8.1 - - - -
124A LYS* 3.9 28.7 - - + -
125A CYS* 3.6 16.8 - - - -
150A LEU* 4.1 8.7 - - + -
151A CYS* 3.0 6.2 + - - +
153A GLN* 1.3 82.3 - - - +
155A VAL* 1.3 63.8 + - - +
157A ALA* 3.7 6.2 - - - +
158A THR* 3.0 31.9 + - - +
402A ZN 2.3 35.4 - - - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.6 27.1 - - + +
151A CYS 2.8 19.7 + - - +
152A ARG* 3.6 7.0 - - - +
154A CYS* 1.3 77.5 - - - +
156A PHE* 1.3 56.6 + - + +
158A THR* 3.2 8.2 + - - -
159A THR* 2.5 33.2 + - + +
171A ASN* 4.0 9.0 - - - +
174A ALA* 4.0 12.6 - - + +
175A LEU* 3.6 41.7 - - + +
178A MET* 3.9 17.0 - - + -
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 6.3 3.1 - - + -
152A ARG* 3.0 70.2 + - + +
153A GLN* 3.9 4.7 - - - +
155A VAL* 1.3 78.4 - - + +
157A ALA* 1.3 55.5 + - - +
159A THR* 3.7 4.9 - - - -
160A THR* 2.4 58.8 + - + +
175A LEU* 3.9 23.3 - - + -
178A MET* 5.0 3.4 - - + -
179A LYS* 4.0 15.5 - - + -
205A TYR* 4.1 10.8 - + + -
206A CYS* 4.1 31.2 - - + -
230A CYS* 4.7 6.3 - - + -
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Residues in contact with ALA 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A PHE* 6.0 7.2 - - + -
124A LYS* 5.4 6.3 - - - +
153A GLN* 3.2 16.5 + - + +
154A CYS* 3.7 9.2 - - - +
155A VAL 3.3 0.6 - - - -
156A PHE* 1.3 80.0 - - - +
158A THR* 1.3 63.8 + - + +
160A THR* 4.3 10.2 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A LYS* 3.6 33.7 - - + -
150A LEU* 4.0 6.0 - - + +
154A CYS 3.0 18.9 + - - +
155A VAL* 3.2 8.1 + - - -
157A ALA* 1.3 78.8 - - + +
159A THR* 1.3 60.3 + - - +
160A THR 4.9 0.9 - - - -
166A LEU* 3.4 18.4 - - - +
171A ASN* 3.6 27.9 + - - +
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Residues in contact with THR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A VAL 2.5 24.9 + - - +
156A PHE* 3.5 3.3 + - - -
158A THR* 1.3 84.1 - - - +
160A THR* 1.3 68.3 + - - +
161A LYS* 3.5 2.8 + - - +
165A ALA* 3.4 2.4 - - - -
166A LEU* 3.0 42.4 + - + +
171A ASN* 3.4 45.5 - - + +
172A ALA* 3.8 5.6 - - - +
175A LEU* 3.3 26.0 - - + +
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Residues in contact with THR 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A GLY 4.8 4.6 + - - +
60A LEU* 3.7 23.6 - - - +
156A PHE* 2.4 54.5 + - + +
157A ALA* 4.3 10.9 + - - +
158A THR 4.9 0.3 - - - -
159A THR* 1.3 79.2 + - - +
161A LYS* 1.3 60.6 + - - +
165A ALA* 4.0 1.6 - - - -
175A LEU* 4.6 6.1 - - + -
229A ALA 3.2 17.9 - - - +
230A CYS* 4.0 18.8 - - - -
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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