Contacts of the strand formed by residues 165 - 174 (chain B) in PDB entry 4YCG
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 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152B VAL* 3.9 0.3 - - - -
153B LEU* 3.0 46.2 + - + -
154B GLU* 2.7 41.0 + - - +
164B GLY* 1.3 74.1 + - - -
166B LYS* 1.3 69.7 + - - +
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Residues in contact with LYS 166 (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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150B TYR* 3.7 32.5 - - + -
151B ASP 3.6 4.0 - - - -
152B VAL* 4.5 13.2 - - + -
153B LEU* 4.7 0.8 - - - +
154B GLU 5.7 0.2 - - - +
161B GLN* 3.1 53.6 + - - +
163B THR 3.1 18.3 + - - +
164B GLY 4.3 4.9 + - - -
165B THR* 1.3 87.5 - - - +
167B THR* 1.3 61.7 + - - +
168B PHE 4.1 0.8 + - - -
204B GLU* 3.4 26.4 + - + +
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Residues in contact with THR 167 (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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150B TYR* 4.5 1.3 - - - -
151B ASP* 2.8 58.4 + - + +
153B LEU* 3.6 27.8 - - + -
166B LYS* 1.3 74.1 - - - +
168B PHE* 1.3 64.6 + - - +
169B LEU* 3.8 0.7 - - - +
190B ARG* 3.6 26.1 + - - +
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Residues in contact with PHE 168 (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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148B VAL* 3.5 28.0 - - + -
150B TYR* 3.7 22.6 - + + -
166B LYS 4.1 1.4 + - - -
167B THR* 1.3 78.2 + - - +
169B LEU* 1.3 76.1 + - - +
170B VAL* 3.5 17.9 - - - -
171B SER* 3.3 32.1 - - - -
190B ARG* 5.7 0.9 + - - -
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Residues in contact with LEU 169 (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 VAL* 3.0 21.7 + - + +
150B TYR 3.9 4.3 - - - -
151B ASP* 3.4 39.0 - - + +
167B THR 4.0 2.2 - - - +
168B PHE* 1.3 89.1 - - - +
170B VAL* 1.3 68.1 + - + +
183B GLU 5.0 0.8 - - - +
184B VAL* 3.7 33.7 - - + -
186B SER* 4.4 8.1 - - - -
187B ALA* 3.7 27.6 - - + +
190B ARG* 3.9 16.8 - - - +
203B LEU* 4.3 4.0 - - + -
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Residues in contact with VAL 170 (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 MET 4.0 0.3 - - - +
148B VAL* 3.4 4.7 - - - -
149B VAL* 3.1 37.0 + - + +
168B PHE* 3.5 8.0 - - - -
169B LEU* 1.3 86.4 - - - +
171B SER* 1.3 74.9 + - - +
172B GLN* 4.5 3.7 - - + +
182B LEU* 4.0 24.0 - - + +
183B GLU* 3.1 42.2 - - + +
184B VAL* 4.2 7.2 - - + -
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Residues in contact with SER 171 (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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146B SER* 5.6 2.9 - - - -
147B MET 3.8 3.1 - - - -
148B VAL* 4.0 12.5 - - - +
168B PHE* 3.3 22.8 - - - -
170B VAL* 1.3 79.7 - - - +
172B GLN* 1.3 61.9 + - - +
173B ASP* 4.3 3.4 + - - -
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Residues in contact with GLN 172 (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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146B SER* 3.3 2.2 - - - -
147B MET* 2.7 69.5 + - + +
170B VAL* 4.5 3.6 - - + +
171B SER* 1.3 77.8 + - - +
173B ASP* 1.3 87.7 + - - +
174B ILE* 3.8 3.3 + - + -
180B GLU* 4.0 17.5 + - - +
181B THR 4.1 8.1 - - - +
182B LEU* 3.6 28.8 - - + +
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Residues in contact with ASP 173 (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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144B GLU* 5.8 1.6 - - - +
145B GLY 3.7 5.8 - - - +
146B SER* 3.3 17.3 - - - -
171B SER* 4.3 3.1 + - - -
172B GLN* 1.3 96.3 + - - +
174B ILE* 1.3 59.0 + - - +
175B ARG* 5.5 4.4 + - + +
180B GLU* 5.0 0.9 - - - +
210B HIS* 4.6 1.6 - - - -
304B ZN 2.1 37.2 - - - -
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Residues in contact with ILE 174 (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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131B VAL* 3.6 46.4 - - + -
143B LEU* 5.6 1.6 - - + -
144B GLU* 3.8 3.6 - - - +
145B GLY 2.9 44.7 + - - +
146B SER 3.7 9.2 - - - +
147B MET* 4.1 17.9 - - + +
172B GLN* 4.1 11.2 - - + +
173B ASP* 1.3 78.5 - - - +
175B ARG* 1.3 71.8 + - - +
176B ASP 5.3 0.2 - - - +
180B GLU* 4.4 11.0 - - + +
207B VAL* 4.6 7.2 - - + -
217B LEU* 3.7 25.8 - - + -
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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