Contacts of the helix formed by residues 172 - 180 (chain B) in PDB entry 2YVL
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 TYR 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.7 27.6 - + + -
148B ASP* 4.0 12.4 + - - -
149B PHE* 4.1 17.7 - + + -
150B LYS* 4.1 19.5 - - + -
164B VAL* 5.5 0.4 - - + -
166B VAL* 4.0 13.5 - - + -
168B GLU 3.8 16.2 - - - -
169B PRO* 2.9 19.1 + - + +
171B HIS* 1.3 91.1 - + + +
173B LEU* 1.3 59.8 + - - +
174B GLU 3.4 2.7 - - - -
175B LYS* 3.3 9.0 + - + +
176B VAL* 2.9 32.3 + - + +
602B SAM 2.8 34.5 + - - -
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Residues in contact with LEU 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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169B PRO 3.7 1.5 + - - +
170B TRP* 3.5 31.6 + - - +
171B HIS 3.4 2.2 - - - -
172B TYR* 1.3 77.0 - - - +
174B GLU* 1.3 58.0 + - - +
176B VAL* 3.8 4.7 - - + +
177B HIS* 2.8 33.6 + - - +
188B PHE* 3.7 33.4 - - + -
199B LEU* 4.0 10.8 - - + -
202B SER* 3.6 36.3 - - - +
203B ILE* 4.0 11.4 - - + +
206B TYR* 4.0 17.9 - - + -
207B PHE* 4.0 16.3 - - + -
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS 5.0 3.2 + - - +
172B TYR 3.4 0.6 - - - -
173B LEU* 1.3 77.4 - - - +
175B LYS* 1.3 58.4 + - - +
177B HIS* 3.5 3.8 - - + +
178B LYS* 3.0 34.4 + - + +
206B TYR* 3.8 34.4 + - + +
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Residues in contact with LYS 175 (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 PHE* 2.6 46.4 + - + +
150B LYS* 3.0 22.4 + - + +
152B ALA 2.6 27.2 + - - -
154B VAL* 3.4 22.4 - - - +
172B TYR* 3.3 8.9 + - + +
174B GLU* 1.3 75.6 - - - +
176B VAL* 1.3 62.7 + - - +
178B LYS* 3.2 7.5 + - + +
179B SER* 2.7 33.9 + - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 4.5 3.1 - - + -
98B PHE* 3.7 21.5 - - + -
149B PHE* 3.7 20.2 - - + -
162B ALA* 3.9 26.7 - - + -
164B VAL* 4.2 9.0 - - + -
172B TYR* 2.9 24.1 + - + +
173B LEU* 3.9 6.1 - - + +
175B LYS* 1.3 74.0 - - - +
177B HIS* 1.3 63.7 + - - +
179B SER* 3.1 16.7 + - - -
180B LEU* 3.2 16.4 + - + +
186B VAL* 4.2 8.3 - - + -
188B PHE* 5.7 2.2 - - + -
207B PHE* 4.2 15.5 - - + -
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Residues in contact with HIS 177 (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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173B LEU 2.8 20.0 + - - +
174B GLU* 3.5 5.6 - - + +
176B VAL* 1.3 76.2 - - - +
178B LYS* 1.3 63.8 + - + +
180B LEU* 3.3 6.9 + - - -
206B TYR* 3.0 47.9 + + + +
207B PHE* 3.9 14.5 - - + -
245B LYS* 2.8 53.5 + - + +
246B LEU 2.9 27.4 + - - -
248B THR* 3.2 27.8 + - + +
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Residues in contact with LYS 178 (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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156B GLU* 3.1 50.4 + - + +
157B GLY* 2.9 20.4 + - - -
174B GLU* 3.0 24.8 + - + +
175B LYS* 3.2 9.4 + - + +
177B HIS* 1.3 81.7 - - + +
179B SER* 1.3 58.5 + - - +
180B LEU 3.4 2.1 + - - +
245B LYS* 4.4 5.7 + - - +
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Residues in contact with SER 179 (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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96B LEU* 4.3 9.4 - - - -
149B PHE* 4.0 7.8 - - - -
154B VAL* 3.6 29.4 + - - +
155B PRO 4.1 4.7 - - - +
156B GLU* 4.3 1.3 - - - +
157B GLY 3.5 5.2 - - - +
158B ILE 3.2 21.8 + - - -
159B PHE* 3.2 22.2 + - - -
175B LYS* 2.7 26.4 + - - +
176B VAL 3.1 6.0 + - - -
178B LYS* 1.3 75.8 - - - +
180B LEU* 1.3 57.2 - - - +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B LEU* 5.7 0.9 - - + -
157B GLY* 3.5 11.0 - - - -
159B PHE* 3.6 18.2 - - + +
161B ALA* 3.5 36.6 - - - +
162B ALA* 3.8 7.4 - - + +
176B VAL* 3.2 18.5 + - + +
177B HIS 3.6 7.9 - - - +
178B LYS 3.2 1.2 - - - +
179B SER* 1.3 79.5 - - - +
181B MET* 1.3 59.8 + - - +
182B GLU* 4.0 0.7 + - - +
184B ALA* 4.0 10.3 - - + +
185B PRO 4.2 11.4 - - - +
186B VAL* 4.3 3.4 - - + -
207B PHE* 3.5 35.9 - - + -
245B LYS* 2.7 35.7 + - + -
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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