Contacts of the strand formed by residues 204 - 210 (chain W) 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 THR 204 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123W GLY* 4.3 11.7 - - - -
124W PRO* 3.2 23.6 - - + +
198W ASN* 3.1 6.8 - - - +
199W HIS* 2.9 31.5 + - - +
202W SER* 2.5 36.2 + - - +
203W ASN* 1.3 74.7 - - - +
205W LYS* 1.3 62.3 + - - +
206W VAL* 5.5 5.2 - - + -
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Residues in contact with LYS 205 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L ASP* 3.6 15.3 + - - +
152L ASN* 3.6 18.7 + - - +
153L ALA* 3.1 25.8 - - + +
154L LEU* 2.5 34.5 + - - +
197W VAL 3.3 12.3 - - - +
198W ASN* 3.5 30.5 - - + +
200W LYS* 5.7 3.2 - - - +
203W ASN 4.3 2.6 + - - +
204W THR* 1.3 78.0 - - - +
206W VAL* 1.3 58.2 + - - +
207W ASP* 5.5 0.4 - - - +
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Residues in contact with VAL 206 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L ALA* 5.1 0.2 - - - +
154L LEU* 3.2 29.6 - - + +
156L SER* 5.6 4.5 - - - -
124W PRO 6.1 0.7 - - - +
126W VAL* 3.6 37.2 - - + -
197W VAL* 2.8 50.5 + - + +
204W THR* 5.2 4.5 - - + -
205W LYS* 1.3 84.3 - - - +
207W ASP* 1.3 74.6 + - - +
208W LYS* 4.9 1.6 - - + -
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Residues in contact with ASP 207 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L VAL* 4.9 1.6 - - - +
153L ALA* 3.8 14.4 - - - +
154L LEU 3.1 6.2 + - - +
155L GLN* 3.0 31.4 + - - +
156L SER* 3.2 26.7 + - - +
158L ASN* 5.0 0.2 + - - -
181L LEU* 5.5 1.6 - - - +
189L HIS* 4.7 11.8 + - - -
194W ILE* 3.1 27.9 - - + +
195W CYS 3.3 4.7 - - - -
196W ASN* 3.0 26.5 + - - +
205W LYS* 5.5 0.3 - - - +
206W VAL* 1.3 83.4 - - - +
208W LYS* 1.3 60.3 + - - +
209W LYS 3.9 0.3 + - - -
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Residues in contact with LYS 208 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156L SER* 3.5 29.1 + - - +
157L GLY* 3.9 16.2 - - - +
123V GLU* 3.7 23.2 + - - -
126W VAL* 3.5 49.8 - - + +
128W PRO* 4.2 22.0 - - + +
139W CYS* 4.5 3.6 - - - -
193W TYR 3.9 0.2 - - - +
194W ILE* 3.3 2.8 - - - +
195W CYS* 2.8 46.9 + - - +
206W VAL* 4.1 2.6 - - + +
207W ASP* 1.3 71.5 - - - +
209W LYS* 1.3 76.2 + - - +
210W VAL* 3.6 3.0 + - + +
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Residues in contact with LYS 209 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171H SER* 4.8 7.5 + - - -
156L SER 3.1 9.0 + - - +
157L GLY* 3.7 30.3 + - - +
158L ASN* 4.0 19.3 - - + +
180L THR* 5.0 10.5 + - - +
181L LEU* 5.3 0.6 - - + +
128W PRO* 4.4 2.9 - - - +
192W THR* 3.5 33.7 + - + +
193W TYR 3.4 12.8 - - - +
194W ILE* 4.1 8.7 - - + +
207W ASP 3.9 1.0 + - - -
208W LYS* 1.3 86.9 + - - +
210W VAL* 1.3 67.8 + - - +
211W GLU* 4.1 26.8 + - + +
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Residues in contact with VAL 210 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128W PRO* 3.5 22.2 - - + -
129W LEU 3.6 29.2 - - - +
130W ALA* 4.2 3.4 - - - -
137W LEU* 3.6 30.2 - - + +
138W GLY 3.0 23.3 - - - +
139W CYS* 4.4 7.4 - - - -
153W TRP* 4.6 4.7 - - + -
193W TYR* 2.8 28.8 + - - +
208W LYS 4.2 8.7 - - - +
209W LYS* 1.3 77.4 - - - +
211W GLU* 1.3 69.5 + - - +
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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