Contacts of the strand formed by residues 189 - 195 (chain B) in PDB entry 4F9P
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 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150B TRP* 4.3 23.7 - - + -
151B SER 3.3 11.0 - - - +
152B ASN* 4.8 2.2 - - - +
158B ILE* 5.7 7.2 - - + -
181B MET* 5.2 14.1 - - + -
188B GLY* 1.3 73.1 - - - -
190B SER* 1.3 59.2 + - - +
204B ALA 4.1 0.3 - - - +
205B SER* 3.5 0.2 - - - -
206B ILE* 2.8 37.0 + - + +
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Residues in contact with SER 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B GLN 3.8 0.5 - - - +
150B TRP* 3.4 3.4 - - - -
151B SER* 2.6 55.5 + - - +
152B ASN 4.5 3.1 + - - -
188B GLY 4.7 2.3 + - - -
189B VAL* 1.3 75.3 - - - +
191B CYS* 1.3 61.6 + - - +
192B THR* 3.9 1.0 + - - -
203B THR* 5.5 5.2 - - - -
204B ALA 3.1 14.8 - - - -
205B SER* 3.8 16.2 - - - -
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Residues in contact with CYS 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 5.1 2.7 - - - -
137B CYS* 2.0 50.3 - - + -
148B ILE* 4.5 9.6 - - + -
149B GLN 3.7 6.3 - - - +
150B TRP* 3.9 25.4 - - + +
190B SER* 1.3 72.8 - - - +
192B THR* 1.3 65.4 + - - +
193B ILE* 4.6 12.8 - - - -
203B THR* 3.3 2.5 - - - -
204B ALA* 3.0 35.5 + - + +
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B GLN 4.4 1.0 - - - +
148B ILE* 4.0 1.9 - - - -
149B GLN* 3.0 31.1 + - - +
151B SER* 6.3 2.2 - - - -
190B SER* 5.0 2.2 - - - -
191B CYS* 1.3 77.2 - - - +
193B ILE* 1.3 61.9 + - - +
194B ARG* 3.5 9.5 + - - +
201B GLU* 5.5 8.3 - - - -
202B LYS 3.6 6.1 - - - -
203B THR* 4.2 13.7 - - - -
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Residues in contact with ILE 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B LEU* 4.9 11.0 - - + -
137B CYS* 5.1 3.8 - - - -
138B ARG 5.2 0.9 - - - +
139B SER* 3.6 31.2 - - - +
142B TRP* 4.0 32.4 - - + +
146B PRO* 5.4 5.6 - - + -
148B ILE* 3.9 30.7 - - + -
175B VAL* 4.8 13.0 - - + +
191B CYS* 4.6 15.3 - - - -
192B THR* 1.3 70.0 - - - +
194B ARG* 1.3 60.3 + - - +
201B GLU* 4.2 0.2 - - - -
202B LYS* 2.9 33.7 + - + +
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B TRP* 5.4 0.4 - - - -
146B PRO* 2.7 31.7 - - - +
147B GLN 3.7 13.5 + - - +
192B THR* 3.5 8.2 + - - +
193B ILE* 1.3 75.4 - - - +
195B SER* 1.3 56.5 + - - +
196B SER* 4.1 1.4 + - - -
200B LEU 4.1 0.7 - - - -
201B GLU* 3.1 38.6 - - + +
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA* 5.7 0.7 - - - +
116B ALA 5.9 0.2 - - - -
142B TRP* 4.5 14.6 - - - -
143B TYR 4.1 9.7 + - - -
144B PRO* 3.9 22.9 + - - +
146B PRO* 3.8 10.2 - - - +
193B ILE 4.2 0.4 + - - -
194B ARG* 1.3 76.9 - - - +
196B SER* 1.3 58.8 + - - +
197B LEU* 3.3 10.0 + - - +
198B LEU* 4.6 12.1 - - - -
199B GLY* 3.7 1.0 + - - -
200B LEU* 3.1 30.9 + - - +
201B GLU* 5.1 1.0 - - - +
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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