Contacts of the helix formed by residues 135 - 140 (chain A) in PDB entry 1RYF
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 LYS 135 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ALA* 3.0 23.2 + - - +
14A VAL 3.4 23.8 - - - +
102A SER* 3.7 18.4 + - - +
103A LEU* 4.5 3.3 - - - +
104A VAL* 4.6 6.0 - - + +
134A THR* 1.3 80.3 - - - +
136A LEU* 1.3 65.1 + - - +
137A ASP* 3.1 14.1 - - - -
138A LEU* 3.0 35.1 + - + +
139A ARG 3.7 2.9 + - - -
176A CYS 3.1 4.6 + - - -
177A SER* 4.5 0.2 - - - +
178A ALA 5.2 0.2 - - - +
538A GDP 3.1 63.3 + - + +
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Residues in contact with LEU 136 (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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103A LEU* 3.5 22.0 - - + -
134A THR 3.3 1.2 - - - -
135A LYS* 1.3 77.5 - - - +
137A ASP* 1.3 60.7 + - - +
138A LEU 3.1 1.7 + - - -
139A ARG* 3.2 43.3 + - - +
140A ASP* 4.4 7.1 + - - +
175A GLU* 4.0 26.7 - - + +
176A CYS* 2.9 22.5 + - - +
177A SER* 4.0 1.3 - - - +
182A ARG* 3.4 55.0 + - + +
183A GLY 5.6 0.2 - - - +
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Residues in contact with ASP 137 (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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135A LYS 3.6 3.5 - - - -
136A LEU* 1.3 77.6 - - - +
138A LEU* 1.3 71.5 + - - +
140A ASP* 4.6 2.5 + - - +
141A ASP* 4.1 9.4 + - - +
177A SER* 2.6 33.1 + - - +
179A LEU* 3.5 12.9 - - + +
180A THR* 4.1 15.9 - - + +
182A ARG* 5.5 4.0 - - - +
538A GDP 2.7 41.8 + - - +
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Residues in contact with LEU 138 (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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104A VAL* 3.8 32.6 - - + +
135A LYS* 3.0 20.4 + - + +
137A ASP* 1.3 95.3 - - - +
139A ARG* 1.3 64.9 + - - +
140A ASP 3.2 3.1 - - - -
141A ASP* 3.0 28.4 + - + +
144A THR* 3.8 25.6 - - + +
145A ILE* 4.8 0.7 - - - +
538A GDP 3.5 28.0 - - + +
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Residues in contact with ARG 139 (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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103A LEU* 3.8 19.0 - - + +
104A VAL* 4.0 9.6 - - - +
135A LYS 3.7 2.8 + - - -
136A LEU* 3.2 32.1 + - + +
138A LEU* 1.3 77.0 - - - +
140A ASP* 1.3 70.1 + - - +
145A ILE* 3.6 18.5 - - - +
155A PRO* 3.7 19.0 - - + +
156A ILE 2.9 30.4 + - - -
157A THR* 4.6 4.3 - - - +
158A TYR* 3.5 18.0 - - - +
175A GLU* 2.8 42.9 + - - -
182A ARG* 5.5 2.2 - - - +
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Residues in contact with ASP 140 (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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136A LEU* 4.4 6.8 + - - +
137A ASP 4.6 3.0 + - - +
138A LEU 3.2 0.4 - - - -
139A ARG* 1.3 93.1 + - - +
141A ASP* 1.3 60.9 + - - +
142A LYS* 3.5 17.8 + - - +
145A ILE* 3.9 8.1 - - - +
182A ARG* 5.2 9.5 + - - -
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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