Contacts of the helix formed by residues 133 - 140 (chain F) 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 ASN 133 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124F LEU 4.0 0.9 + - - -
129F GLN* 5.5 3.1 - - - +
131F ASP* 2.7 27.0 + - - +
132F LEU* 1.3 74.0 - - - +
134F VAL* 1.3 62.7 + - - +
135F LYS 3.5 2.0 - - - +
136F ALA* 3.2 30.4 + - - +
430F ASP* 2.9 32.6 + - - +
432F GLY* 3.1 21.6 + - - -
433F ALA 4.4 0.6 - - - +
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Residues in contact with VAL 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F LEU* 3.3 30.5 + - + +
132F LEU* 3.9 23.6 - - + +
133F ASN* 1.3 73.6 - - - +
135F LYS* 1.3 67.5 + - - +
136F ALA 3.1 2.0 - - - -
137F ALA* 2.9 13.0 + - - +
138F TRP* 3.0 49.1 + - + +
215F VAL* 4.1 22.7 - - + +
377F ILE* 4.4 3.8 - - + -
380F LEU* 4.3 3.1 - - + -
431F ALA* 3.7 14.6 - - + -
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Residues in contact with LYS 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 4.1 24.0 - - + -
112F GLU* 2.5 46.2 + - + +
124F LEU 3.9 3.2 + - - -
125F SER* 3.5 30.5 + - - +
133F ASN 3.5 0.6 - - - -
134F VAL* 1.3 76.9 - - - +
136F ALA* 1.3 52.4 + - - +
138F TRP* 3.1 18.9 + - + +
139F ALA* 2.7 36.5 + - + +
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Residues in contact with ALA 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASN* 3.2 38.6 + - - +
134F VAL 3.1 0.4 - - - -
135F LYS* 1.3 80.4 - - - +
137F ALA* 1.3 58.5 + - - +
139F ALA* 3.6 8.0 + - - +
140F GLN* 3.2 31.8 + - - +
432F GLY* 4.1 5.6 - - - -
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Residues in contact with ALA 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ASN 3.8 1.0 + - - -
134F VAL 2.9 10.2 + - - +
136F ALA* 1.3 77.4 - - - +
138F TRP* 1.3 65.6 + - - +
140F GLN* 3.1 13.4 + - - +
141F GLY 3.4 0.5 + - - -
142F TYR* 3.1 19.6 + - - +
380F LEU* 3.8 24.7 - - + -
431F ALA* 4.0 15.3 - - + +
432F GLY* 4.1 0.6 - - - -
435F VAL* 3.9 29.6 - - + -
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Residues in contact with TRP 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 3.2 44.1 - + + +
113F PRO* 3.7 19.7 - - + -
118F PHE* 3.8 28.7 - + - -
124F LEU* 4.1 8.3 - - + -
125F SER* 5.5 0.4 - - - -
134F VAL* 3.0 32.6 + - + +
135F LYS* 3.4 26.0 - - + +
137F ALA* 1.3 75.8 - - - +
139F ALA* 1.3 55.5 + - - +
141F GLY* 2.7 25.8 + - - -
142F TYR 3.2 21.6 + - - +
143F THR* 4.2 8.1 - - + +
213F VAL* 3.8 11.9 - - + -
214F GLY 3.8 16.6 - - - -
215F VAL* 2.9 21.6 + - - -
217F TYR* 3.4 23.5 - + - +
380F LEU* 4.5 3.1 - - + +
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 4.1 29.6 - - + +
135F LYS* 2.7 20.8 + - + +
136F ALA* 3.7 10.1 - - - +
138F TRP* 1.3 73.6 - - - +
140F GLN* 1.3 57.9 + - + +
141F GLY* 3.2 4.0 + - - -
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Residues in contact with GLN 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136F ALA* 3.2 17.8 + - - +
137F ALA 3.1 9.9 + - - +
139F ALA* 1.3 76.8 - - + +
141F GLY* 1.3 57.0 + - - +
142F TYR* 3.7 20.7 + - + -
432F GLY* 3.1 30.5 + - - -
435F VAL* 3.3 16.9 - - - +
436F ALA* 3.8 18.8 - - - +
439F GLN* 4.1 10.0 + - - +
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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