Contacts of the strand formed by residues 218 - 224 (chain A) in PDB entry 5TOL
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 VAL 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A ARG* 3.7 9.9 - - - -
56A GLY* 2.8 53.4 + - - +
57A LYS 3.7 6.3 - - - +
58A SER* 4.1 23.8 - - - +
61A GLY 4.4 2.9 - - - +
62A TYR* 3.5 30.5 - - + +
204A GLY* 3.1 31.4 - - - +
217A SER* 1.3 78.2 + - - +
219A GLY* 1.3 57.5 + - - +
387A GLU* 5.3 1.3 - - - +
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Residues in contact with GLY 219 (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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52A ASP* 4.7 1.8 - - - -
54A LEU 3.4 15.0 - - - -
55A ARG* 3.9 7.9 - - - -
62A TYR* 3.3 14.9 - - - -
203A CYS* 3.0 28.9 + - - +
204A GLY* 3.9 4.8 - - - +
218A VAL* 1.3 76.4 - - - +
220A GLY* 1.3 57.8 + - - -
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Residues in contact with GLY 220 (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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52A ASP* 3.0 29.1 + - - -
54A LEU* 3.2 22.7 + - - +
201A GLN* 3.0 14.1 - - - -
203A CYS* 4.1 11.9 - - - -
219A GLY* 1.3 74.6 - - - -
221A SER* 1.3 63.1 + - - -
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Residues in contact with SER 221 (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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50A MET 4.2 0.2 - - - -
51A VAL* 3.5 7.6 - - - +
52A ASP* 2.8 25.6 + - - +
53A ASN* 3.4 4.5 - - - -
54A LEU* 3.7 6.9 - - - +
199A SER 3.7 0.9 - - - +
200A LEU* 3.5 3.6 - - - -
201A GLN* 2.8 42.1 + - - +
220A GLY* 1.3 74.3 - - - -
222A MET* 1.3 60.0 + - - +
223A ILE* 3.9 12.7 - - - +
231A LEU* 3.9 27.6 - - - +
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Residues in contact with MET 222 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A MET* 4.0 2.9 - - - +
53A ASN* 2.7 34.3 + - - +
54A LEU* 3.7 9.8 - - + +
64A VAL* 5.0 7.4 - - + -
79A VAL* 4.1 22.2 - - - -
135A ILE* 6.0 2.2 - - + -
167A LEU* 4.6 8.5 - - + -
169A LEU* 3.4 40.6 - - + -
184A PHE* 6.5 0.4 - - + -
185A PHE* 4.7 2.7 - - + -
198A PHE* 4.0 15.3 - - + -
199A SER 3.3 5.6 - - - +
200A LEU* 3.6 18.6 - - + -
221A SER* 1.3 72.2 - - - +
223A ILE* 1.3 61.9 + - - +
224A ILE* 3.4 34.2 + - + +
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Residues in contact with ILE 223 (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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47A PHE* 3.6 42.6 - - + +
50A MET* 4.0 20.6 - - + -
51A VAL* 4.2 4.7 - - + +
198A PHE* 3.1 5.9 - - - -
199A SER* 2.9 51.6 + - - +
221A SER* 4.1 12.3 - - - -
222A MET* 1.3 69.1 - - - +
224A ILE* 1.3 57.8 + - - +
226A GLY 3.3 25.3 - - - +
227A ILE 4.0 1.8 - - - +
228A ASP* 4.2 10.1 - - + +
231A LEU* 4.0 24.2 - - + -
390A TYR* 3.9 9.6 - - + +
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Residues in contact with ILE 224 (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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47A PHE* 4.0 2.4 - - - -
50A MET* 3.4 24.2 - - - +
53A ASN* 4.6 3.1 - - - +
64A VAL* 5.6 0.7 - - + -
135A ILE* 4.1 27.8 - - + -
138A GLY* 4.3 9.6 - - - -
139A PRO* 3.8 29.5 - - + +
185A PHE* 3.9 9.4 - - + -
188A LEU* 3.8 28.5 - - + -
194A VAL* 3.9 8.7 - - + +
198A PHE* 4.1 3.8 - - - -
222A MET* 3.4 53.3 + - + +
223A ILE* 1.3 70.2 - - - +
225A GLY* 1.3 61.3 + - - +
226A GLY 3.5 0.6 + - - -
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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