Contacts of the helix formed by residues 117 - 121 (chain E) in PDB entry 4RYD
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 117 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E PRO* 1.3 80.5 + - + +
118E PHE* 1.3 67.4 + - - +
119E PRO* 3.2 3.6 - - - -
120E GLN* 2.8 43.6 + - - +
121E GLN* 3.4 7.3 + - - +
211E CYS* 2.8 26.9 + - - +
212E GLY* 3.8 4.7 - - - +
352E VAL* 3.9 11.7 - - + -
360E CYS* 3.7 25.1 - - - -
362E GLU* 2.9 36.8 - - + +
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Residues in contact with PHE 118 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112E GLU* 3.6 32.1 - - + -
113E PRO* 3.7 33.2 - - + +
115E ASP* 3.1 18.5 + - + +
117E LYS* 1.3 76.3 - - - +
119E PRO* 1.3 72.9 - - + +
121E GLN* 2.9 37.5 + - + +
124E LEU* 4.3 14.4 - - + -
125E SER* 3.9 25.2 - - - +
135E LYS* 5.0 0.7 - - + -
138E TRP* 3.9 32.1 - + - -
211E CYS 4.1 2.0 + - - -
212E GLY* 4.1 1.2 - - - -
213E VAL* 4.2 9.4 - - + -
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Residues in contact with PRO 119 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E ASP 3.6 4.5 - - - +
116E PRO 3.4 14.4 - - - +
117E LYS 3.2 5.6 - - - -
118E PHE* 1.3 101.0 - - + +
120E GLN* 1.3 66.2 + - - +
121E GLN 3.5 0.7 + - - -
122E TRP* 4.4 6.4 + - - +
125E SER 5.5 1.9 - - - +
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Residues in contact with GLN 120 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116E PRO 3.6 17.2 + - - +
117E LYS* 2.8 42.9 + - + +
119E PRO* 1.3 84.7 - - - +
121E GLN* 1.3 57.9 + - - +
122E TRP* 2.9 27.0 + - - +
349E LYS* 5.4 2.9 - - + +
352E VAL* 3.9 20.5 - - + +
362E GLU* 4.1 15.1 + - - +
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Residues in contact with GLN 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E LYS 3.7 8.7 - - - +
118E PHE* 2.9 23.9 + - + +
119E PRO 3.2 1.3 - - - -
120E GLN* 1.3 74.6 - - - +
122E TRP* 1.3 58.5 + - - +
123E TYR* 3.2 23.0 + - + +
124E LEU* 3.0 39.9 + - + +
125E SER 3.6 7.8 + - - +
200E GLY 5.8 0.4 + - - -
201E GLU* 6.2 1.0 - - - +
212E GLY* 3.5 12.0 - - - -
213E VAL* 2.9 52.3 + - - +
352E VAL* 3.2 31.8 + - + -
353E THR* 5.3 0.4 - - - +
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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