Contacts of the strand formed by residues 218 - 222 (chain A) in PDB entry 4CBS
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 SER 218 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A VAL* 3.3 9.2 - - - +
78A ILE* 2.8 38.9 + - - +
80A GLY 2.8 14.2 + - - -
81A SER 3.2 12.8 + - - -
82A GLY* 4.1 2.9 - - - -
85A ALA* 3.2 26.0 - - - +
205A SER 3.2 14.6 - - - -
206A GLY* 4.3 3.1 - - - -
207A SER 4.5 1.1 - - - +
217A THR* 1.3 77.4 - - - +
219A LEU* 1.3 63.8 + - - +
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Residues in contact with LEU 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.0 35.7 - - + -
67A VAL* 4.4 8.3 - - + -
68A PHE* 3.9 13.0 - - + -
76A LEU 3.8 2.0 - - - -
77A VAL* 4.3 0.9 - - + -
85A ALA* 4.4 1.3 - - - +
188A LEU* 4.3 14.1 - - + -
204A TYR* 3.0 9.6 - - - +
205A SER 2.9 38.1 + - - +
206A GLY 4.9 3.1 - - - +
207A SER 5.8 0.2 - - - +
211A LEU* 4.0 26.2 - - + -
217A THR* 5.5 0.2 - - - +
218A SER* 1.3 83.5 - - - +
220A ILE* 1.3 61.9 + - - +
272A LEU* 3.8 32.1 - - + -
276A LEU* 4.6 4.7 - - + -
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Residues in contact with ILE 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ILE* 4.9 0.4 - - - +
68A PHE* 4.0 4.2 - - - -
75A THR* 3.3 4.3 - - - +
76A LEU* 2.8 69.4 + - + +
78A ILE* 3.9 13.0 - - + -
85A ALA* 3.5 26.2 - - + +
88A ALA* 4.7 4.7 - - + -
89A ALA* 4.0 14.4 - - + +
202A ILE* 4.2 6.1 - - + -
203A LEU 3.3 12.6 - - - +
204A TYR* 3.9 8.5 - - + -
219A LEU* 1.3 75.5 - - - +
221A SER* 1.3 62.7 + - - +
222A PHE* 3.5 35.4 - - + -
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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
----------------------------------------------------------
68A PHE* 3.7 15.7 - - - -
70A THR* 3.7 2.1 - - - +
72A ASN* 3.4 16.1 + - - +
74A LEU 3.4 4.7 - - - -
75A THR* 2.3 27.2 + - - -
195A MET* 3.4 23.8 - - - +
202A ILE* 3.5 6.1 - - - +
203A LEU 2.9 27.7 + - - +
220A ILE* 1.3 75.5 - - - +
222A PHE* 1.3 65.5 + - - +
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Residues in contact with PHE 222 (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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72A ASN* 3.0 20.6 + - - +
73A PRO* 5.4 0.7 - - - +
74A LEU* 2.7 52.2 + - + +
76A LEU* 5.2 0.7 - - + -
88A ALA* 5.3 2.7 - - + -
89A ALA* 4.4 12.8 - - - -
92A ASN* 5.7 0.4 - - - -
93A VAL* 4.7 1.1 - - + -
201A ASP 3.4 3.1 - - - -
202A ILE* 3.7 33.0 - - + -
220A ILE* 3.5 39.3 - - + -
221A SER* 1.3 75.8 + - - +
223A SER* 1.3 65.5 + - - +
226A ALA* 3.9 9.0 - - + -
227A LYS* 5.1 0.3 - - - +
230A MET* 3.4 31.6 - - + -
244A ILE* 3.7 29.2 - - + -
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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