Contacts of the strand formed by residues 151 - 156 (chain L) in PDB entry 4WEB
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 151 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149L ASP 5.2 1.3 - - - +
150L ILE* 1.3 92.1 + - - +
152L VAL* 1.3 66.6 + - - +
201L GLU 3.5 0.7 - - - +
202L ALA* 3.5 4.0 - - - -
203L THR* 3.0 49.7 + - - +
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Residues in contact with VAL 152 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L CYS* 5.8 0.4 - - - -
142L LEU* 3.5 42.4 - - + -
151L ASN* 1.3 75.9 - - - +
153L LYS* 1.3 61.8 + - - +
154L TRP* 3.9 8.7 + - + -
165L VAL* 5.2 1.1 - - + -
167L ASN* 3.6 31.4 - - - +
181L MET* 3.8 15.3 - - + -
183L SER* 3.7 12.3 - - - +
200L CYS* 5.7 5.4 - - + -
201L GLU 3.2 8.3 - - - +
202L ALA* 4.8 0.7 - - + -
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Residues in contact with LYS 153 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151L ASN 4.2 0.4 - - - -
152L VAL* 1.3 72.2 - - - +
154L TRP* 1.3 63.7 + - - +
155L LYS* 3.5 2.7 + - + -
160L GLU* 5.7 7.4 - - + -
200L CYS* 3.3 1.7 - - - -
201L GLU* 2.6 62.7 + - + +
203L THR* 5.4 4.2 + - + +
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Residues in contact with TRP 154 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123L ILE* 4.0 10.8 - - + -
138L VAL* 3.4 48.9 - - + -
139L VAL 4.1 1.1 - - - -
140L CYS* 3.4 21.3 - - + -
152L VAL* 3.9 8.3 + - + +
153L LYS* 1.3 73.0 - - - +
155L LYS* 1.3 58.4 + - - +
156L ILE* 4.0 0.9 - - + -
160L GLU* 3.6 3.3 - - - -
161L ARG* 2.7 53.4 + - + +
165L VAL* 3.4 30.5 - - + +
183L SER* 2.7 43.5 + - - -
185L LEU* 3.8 27.1 - - + +
198L TYR* 5.2 2.0 - + + -
199L THR 3.3 22.7 - - - -
200L CYS* 3.8 14.3 - - + +
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Residues in contact with LYS 155 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153L LYS* 3.5 5.3 + - + +
154L TRP* 1.3 72.3 - - - +
156L ILE* 1.3 61.0 + - - +
157L ASP 3.9 1.3 + - - -
158L GLY* 4.4 23.3 - - - +
159L SER 3.9 5.6 - - - -
160L GLU* 4.5 1.6 - - - +
198L TYR* 3.7 0.7 - - - -
199L THR* 2.5 55.4 + - + +
201L GLU* 4.6 16.6 - - - +
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Residues in contact with ILE 156 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L TRP* 3.9 2.6 + - + -
155L LYS* 1.3 72.6 - - - +
157L ASP* 1.3 73.6 + - - +
158L GLY 3.4 0.2 - - - -
159L SER* 2.5 40.0 + - - +
161L ARG* 4.1 33.9 - - + +
185L LEU* 3.8 13.7 - - + -
187L LEU* 3.7 20.9 - - + -
195L HIS* 4.1 24.9 - - + -
197L SER 3.5 13.2 - - - +
198L TYR* 3.6 31.2 - - + -
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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