Contacts of the strand formed by residues 189 - 198 (chain B) in PDB entry 4YCV
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 ILE 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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351A TYR* 3.7 28.0 - - + +
546A GLY 3.3 26.2 - - - +
548A PRO* 3.6 31.9 - - + -
137B GLY 3.3 7.2 - - - +
138B ARG* 3.4 33.7 - - + +
188B ASP* 1.3 75.0 - - - +
190B VAL* 1.3 63.3 + - - +
213B LEU* 3.6 2.6 - - - +
214B LEU* 2.8 32.1 + - + +
215B SER* 2.9 29.2 + - - +
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B ILE 4.1 0.3 - - - +
136B THR* 3.5 3.1 - - - -
137B GLY 2.9 28.7 + - - +
139B ILE* 3.9 14.8 - - + -
154B LEU* 3.8 24.7 - - + -
184B ILE* 4.2 25.6 - - + -
188B ASP* 4.6 7.4 - - + -
189B ILE* 1.3 78.9 - - - +
191B GLY* 1.3 62.8 + - - +
192B ILE* 4.1 13.5 - - + +
211B THR* 4.0 6.3 - - + -
212B ILE 3.3 13.7 - - - +
213B LEU* 4.0 18.2 - - + -
214B LEU* 3.9 4.5 - - - -
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Residues in contact with GLY 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.8 24.2 - - - -
135B ILE 3.7 5.2 - - - -
136B THR* 4.4 0.2 - - - -
190B VAL* 1.3 74.0 - - - +
192B ILE* 1.3 64.6 + - - +
211B THR* 3.6 0.7 - - - +
212B ILE* 2.8 39.5 + - - +
214B LEU* 3.4 15.2 - - - +
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Residues in contact with ILE 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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106B PHE* 3.5 2.6 - - - -
133B LEU 3.5 1.7 - - - +
134B ASN* 3.3 2.4 - - - -
135B ILE* 2.8 46.2 + - + +
139B ILE* 5.4 0.9 - - + -
154B LEU* 3.9 15.9 - - + -
163B VAL* 3.7 36.8 - - + -
190B VAL* 4.1 15.9 - - + +
191B GLY* 1.3 79.5 - - - +
193B VAL* 1.3 66.0 + - - +
206B ILE* 4.0 23.1 - - + -
208B PRO* 3.6 24.7 - - + -
210B GLU 3.7 3.4 - - - -
211B THR* 3.7 16.8 - - + +
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 4.0 16.6 - - + -
132B ILE* 3.8 17.5 - - + -
133B LEU 3.4 2.5 - - - -
134B ASN* 3.3 32.8 - - - +
192B ILE* 1.3 73.5 - - - +
194B GLY* 1.3 59.2 + - - +
208B PRO* 4.2 1.6 - - - -
209B LYS* 2.9 36.2 + - + +
210B GLU* 2.8 38.6 + - + +
212B ILE* 6.1 0.9 - - + +
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Residues in contact with GLY 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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132B ILE* 4.4 8.1 - - - -
133B LEU* 2.9 32.8 + - - +
192B ILE* 3.9 3.0 + - - +
193B VAL* 1.3 76.4 - - - +
195B PHE* 1.3 62.6 + - - -
206B ILE* 3.5 12.6 - - - +
207B PHE 3.1 14.6 - - - -
208B PRO* 3.8 2.5 - - - -
209B LYS* 3.8 6.5 - - - -
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Residues in contact with PHE 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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127B HIS* 4.1 11.4 - + - -
128B LEU 3.4 15.0 - - - +
129B GLU* 4.0 29.8 - - + +
131B THR 3.1 20.0 - - - +
132B ILE* 4.8 5.2 - - + -
169B PHE* 3.4 47.3 - + + -
194B GLY* 1.3 74.6 - - - -
196B PRO* 1.3 75.4 - - - +
206B ILE* 3.6 3.1 - - - -
207B PHE* 2.9 61.3 + + + -
209B LYS* 5.7 4.3 - - + -
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Residues in contact with PRO 196 (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 PHE* 3.9 24.7 - - + -
119B TYR* 3.6 42.6 - - + +
128B LEU* 3.4 25.6 + - + +
131B THR* 3.2 18.4 - - + +
133B LEU* 4.2 13.5 - - + -
194B GLY 4.3 0.2 - - - +
195B PHE* 1.3 102.3 - - + +
197B GLY* 1.3 58.2 + - - +
205B SER 3.7 6.5 - - - +
206B ILE* 4.0 0.4 - - + -
207B PHE* 4.1 0.4 - - - -
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Residues in contact with GLY 197 (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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122B LEU* 4.1 12.2 - - - +
126B GLU 3.2 13.2 - - - -
127B HIS* 4.2 2.5 - - - -
196B PRO* 1.3 77.3 - - - +
198B LYS* 1.3 60.6 + - - -
204B LEU* 3.3 9.2 - - - +
205B SER 2.9 28.8 + - - +
207B PHE* 3.5 14.3 - - - -
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Residues in contact with LYS 198 (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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119B TYR 4.8 2.2 - - - -
120B LYS 2.6 31.1 + - - -
121B ASP* 4.5 2.2 - - - +
122B LEU* 3.3 29.2 + - + +
123B GLY 3.8 15.9 - - - +
124B ASN* 4.1 12.1 + - - +
125B GLY* 3.3 15.6 - - - -
126B GLU 2.8 9.0 + - - +
127B HIS* 4.1 9.2 + - - -
197B GLY* 1.3 73.2 - - - +
199B SER* 1.3 67.5 + - - +
202B GLY* 4.1 18.6 + - - -
203B GLU* 3.7 20.4 - - - +
204B LEU* 3.7 17.0 - - + +
205B SER* 4.3 0.9 - - - +
207B PHE* 4.2 4.0 - - - -
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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