Contacts of the strand formed by residues 204 - 215 (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 LEU 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115B PHE* 3.5 35.4 - - + +
116B ILE* 3.9 36.6 - - + +
119B TYR* 3.8 34.1 - - + +
120B LYS* 4.7 4.3 - - - +
122B LEU* 4.5 1.8 - - + -
160B LYS 6.0 0.2 - - - +
161B ILE* 4.3 6.6 - - + -
162B GLN* 3.4 23.1 + - - +
197B GLY 3.3 20.4 - - - +
198B LYS* 3.7 17.5 - - + +
203B GLU* 1.3 76.0 - - - +
205B SER* 1.3 60.0 + - - +
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Residues in contact with SER 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PHE* 4.1 7.2 - - - -
161B ILE* 5.3 0.4 - - - -
162B GLN* 3.1 28.9 + - - +
164B LEU* 4.3 9.9 - - - +
196B PRO* 3.7 2.3 - - - +
197B GLY* 2.9 38.0 + - - +
199B SER* 3.6 8.2 + - - -
203B GLU 2.9 17.7 + - - -
204B LEU* 1.3 73.2 - - - +
206B ILE* 1.3 60.2 + - - +
207B PHE* 3.8 19.4 - - - -
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Residues in contact with ILE 206 (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* 4.0 22.4 - - + -
133B LEU* 5.1 3.4 - - + +
135B ILE* 4.2 10.8 - - + -
154B LEU* 4.8 4.0 - - + -
161B ILE* 3.7 21.3 - - + -
162B GLN 2.9 16.8 + - - +
163B VAL* 3.5 18.7 - - + -
164B LEU 3.0 21.1 + - - -
192B ILE* 4.0 21.5 - - + -
194B GLY* 3.5 26.7 - - - +
195B PHE 3.5 20.4 - - - +
196B PRO* 4.0 3.1 - - + -
205B SER* 1.3 73.2 - - - +
207B PHE* 1.3 59.5 + - - +
208B PRO* 3.1 6.1 - - - +
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Residues in contact with PHE 207 (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* 3.3 27.4 - + - -
164B LEU* 3.2 50.9 - - + +
169B PHE* 3.9 21.3 - + + -
194B GLY* 3.1 3.1 - - - -
195B PHE* 2.9 72.3 + + + +
197B GLY* 3.5 28.5 - - - -
198B LYS 4.5 7.0 - - - -
199B SER* 5.2 0.7 - - - -
205B SER* 3.8 14.6 - - - -
206B ILE* 1.3 72.7 - - - +
208B PRO* 1.3 67.0 - - - +
209B LYS 3.5 0.5 + - - -
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Residues in contact with PRO 208 (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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163B VAL* 3.8 12.6 - - + -
164B LEU 3.1 17.5 - - - +
165B ALA* 3.9 14.9 - - + -
166B ASN 4.8 2.8 + - - +
169B PHE* 4.5 7.3 - - - +
170B HIS* 4.3 11.1 + - - +
181B TYR* 3.3 19.6 + - - +
192B ILE* 3.6 11.2 - - + -
193B VAL 3.5 6.3 - - - +
194B GLY* 3.8 2.5 - - - -
195B PHE* 5.9 0.2 - - - -
206B ILE 3.1 10.5 - - - +
207B PHE* 1.3 84.0 - - - +
209B LYS* 1.3 61.2 + - - +
210B GLU 3.6 8.5 - - - +
211B THR* 3.1 22.9 - - - +
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Residues in contact with LYS 209 (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* 4.8 24.3 - - + +
169B PHE* 4.0 21.5 - - + +
170B HIS* 3.1 9.2 - - - +
171B ASN* 2.7 54.5 + - + +
193B VAL* 2.9 24.4 + - + +
194B GLY* 3.8 3.8 - - - -
195B PHE* 5.7 4.5 - - + -
207B PHE 3.5 3.8 + - - -
208B PRO* 1.3 73.3 - - - +
210B GLU* 1.3 72.9 + - + +
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Residues in contact with GLU 210 (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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170B HIS* 4.5 5.2 - - + +
171B ASN* 5.1 4.8 + - + +
174B LYS* 4.7 20.6 - - + +
181B TYR* 4.1 2.2 - - - -
193B VAL* 2.8 50.9 + - + +
208B PRO* 3.2 3.0 - - - +
209B LYS* 1.3 96.7 - - + +
211B THR* 1.3 74.5 + - - +
212B ILE* 4.9 13.5 - - + +
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Residues in contact with THR 211 (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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163B VAL* 5.2 0.8 - - + +
170B HIS* 5.4 0.6 + - - -
180B CYS* 3.9 23.9 - - - +
181B TYR* 2.9 34.0 + - + -
183B LYS* 5.4 1.4 + - - -
184B ILE* 3.6 27.5 - - + +
190B VAL* 4.0 11.7 - - + -
191B GLY 3.6 11.2 - - - +
192B ILE* 3.7 16.0 - - + +
208B PRO* 3.1 19.8 - - - +
210B GLU* 1.3 76.1 + - - +
212B ILE* 1.3 62.8 + - - +
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Residues in contact with ILE 212 (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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100B ASN 6.0 0.4 - - - +
103B PRO* 4.3 20.4 - - + -
106B PHE* 3.8 30.7 - - + -
183B LYS* 6.0 0.9 - - - +
184B ILE* 6.3 0.2 - - - -
190B VAL* 3.3 7.9 - - - +
191B GLY* 2.8 43.7 + - - +
193B VAL* 6.1 0.7 - - + -
210B GLU* 4.4 14.3 - - + +
211B THR* 1.3 75.5 - - - +
213B LEU* 1.3 68.7 + - - +
214B LEU* 4.3 5.4 - - + -
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Residues in contact with LEU 213 (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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87B ARG* 3.6 21.3 - - - +
90B PHE* 4.7 7.6 - - + -
100B ASN 4.5 1.6 - - - +
101B PRO* 3.7 25.5 - - + +
103B PRO* 3.4 21.8 - - - +
183B LYS* 4.2 32.0 - - + +
184B ILE* 5.9 4.5 - - + +
188B ASP* 3.9 24.7 - - + +
189B ILE 3.6 17.0 - - - +
190B VAL* 4.0 8.3 - - + -
211B THR 4.4 0.2 + - - -
212B ILE* 1.3 78.2 - - - +
214B LEU* 1.3 59.2 + - - +
215B SER 4.0 9.6 - - - +
216B ALA* 3.9 11.4 - - + +
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Residues in contact with LEU 214 (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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351A TYR* 4.0 28.5 - - + -
509A ASN* 4.4 2.4 + - - -
549A PRO* 4.0 19.4 - - + +
101B PRO 2.8 17.4 - - - +
102B TYR* 3.3 6.4 - - - -
103B PRO* 3.1 29.1 - - + +
106B PHE* 3.7 37.7 - - + +
136B THR* 4.0 6.5 - - + -
189B ILE* 2.8 18.6 + - + +
190B VAL 4.2 2.2 - - - -
191B GLY 3.4 22.9 - - - +
212B ILE* 3.5 10.5 + - + -
213B LEU* 1.3 77.5 - - - +
215B SER* 1.3 60.2 - - - +
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Residues in contact with SER 215 (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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509A ASN* 4.2 2.6 + - - -
546A GLY* 3.3 14.2 - - - +
547A LEU 2.5 34.8 + - - -
548A PRO* 3.8 10.8 - - - -
102B TYR* 3.4 20.0 - - - -
187B GLY 4.9 0.2 - - - +
188B ASP* 3.9 0.2 - - - -
189B ILE* 2.9 44.1 + - - +
213B LEU* 4.1 2.7 - - - -
214B LEU* 1.3 76.2 - - - +
216B ALA* 1.3 61.0 + - - +
217B CYS 3.8 0.2 + - - -
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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