Contacts of the strand formed by residues 218 - 223 (chain Y) in PDB entry 4MXW
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 ARG 218 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118Y GLN* 5.6 8.1 - - - +
120Y SER* 5.6 0.8 + - - -
123Y GLU* 2.7 72.9 + - - +
124Y GLY 4.5 4.9 + - - -
125Y LEU 3.2 7.9 - - - +
126Y ALA* 3.8 22.6 - - + +
163Y LEU* 2.5 41.9 - - + +
216Y GLY 3.7 8.0 + - - +
217Y GLU* 1.3 79.5 - - - +
219Y VAL* 1.3 62.2 + - - +
220Y TYR* 4.1 2.1 + - + -
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Residues in contact with VAL 219 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124Y GLY* 4.1 0.2 - - - -
125Y LEU* 2.9 43.0 + - + +
127Y LEU* 6.0 1.1 - - + -
135Y LEU* 3.9 23.6 - - + -
161Y SER* 4.1 12.1 - - - -
162Y SER 3.4 8.1 - - - +
163Y LEU 4.4 1.1 - - - -
178Y LEU* 4.0 11.0 - - + -
213Y LEU* 3.6 42.6 - - + -
217Y GLU 4.2 0.9 + - - +
218Y ARG* 1.3 76.6 - - - +
220Y TYR* 1.3 69.6 + - - +
238Y PHE* 4.0 13.9 - - + -
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Residues in contact with TYR 220 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119Y PHE* 6.4 0.4 - - + -
121Y ASP 6.2 0.2 - - - +
123Y GLU 4.6 11.0 - - - -
124Y GLY* 4.0 17.3 - - - +
161Y SER* 3.1 27.0 - - - -
162Y SER* 3.2 34.3 + - - -
163Y LEU* 4.3 15.5 - - + -
175Y PRO* 3.7 26.1 - - + +
218Y ARG* 4.9 1.3 - - + -
219Y VAL* 1.3 75.0 - - - +
221Y VAL* 1.3 76.1 + - - +
222Y ASN* 3.8 27.7 + - + -
238Y PHE* 4.8 5.2 - - - -
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Residues in contact with VAL 221 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102Y LEU* 5.7 1.2 - - + +
104Y TRP* 3.6 36.9 + - + +
137Y CYS* 4.0 19.3 - - + -
159Y LEU* 4.3 1.3 - - + -
160Y ARG 3.5 6.5 - - - +
161Y SER* 4.1 10.8 - - - -
220Y TYR* 1.3 89.5 - - - +
222Y ASN* 1.3 63.2 + - - +
223Y ILE* 4.1 19.5 + - + -
238Y PHE* 3.5 42.2 - - + -
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Residues in contact with ASN 222 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159Y LEU* 3.9 2.1 - - - -
160Y ARG* 2.7 77.3 + - + +
162Y SER* 5.1 0.7 - - - +
220Y TYR* 3.8 26.4 + - + -
221Y VAL* 1.3 74.7 + - - +
223Y ILE* 1.3 71.3 + - - +
224Y SER* 4.4 0.5 + - - -
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Residues in contact with ILE 223 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102Y LEU* 3.7 30.2 - - + +
104Y TRP* 4.9 2.9 - - + -
139Y VAL* 3.5 33.7 - - + -
141Y TYR* 3.3 20.4 - - + +
158Y THR 4.4 2.7 - - - -
159Y LEU* 4.0 16.2 - - + -
221Y VAL* 4.1 10.1 - - + -
222Y ASN* 1.3 84.9 + - - +
224Y SER* 1.3 65.5 + - - +
225Y HIS 3.4 22.2 - - - +
226Y PRO* 3.7 14.0 - - + +
229Y VAL* 4.6 8.1 - - + -
236Y THR* 5.7 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