Contacts of the strand formed by residues 239 - 245 (chain A) 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 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PHE 3.7 2.6 - - - +
190A LEU* 2.9 43.4 + - - +
191A PRO 3.7 5.8 - - - -
192A THR 3.9 8.5 - - - -
193A ALA* 3.5 33.6 - - + +
196A VAL* 3.6 19.1 - - + -
212A VAL* 4.3 9.6 - - + -
213A VAL 3.9 3.8 - - - -
214A GLU* 4.2 11.2 - - + -
236A HIS* 3.6 20.0 - + - -
238A ALA* 1.3 73.1 - - - +
240A LEU* 1.3 63.8 + - - +
241A VAL* 4.1 1.2 + - - +
220B TYR* 3.5 44.1 + + - -
227B PHE* 4.1 12.1 - + - -
220C TYR* 4.1 10.0 + - - -
227C PHE* 5.6 0.2 - - - -
228C ARG* 4.5 0.7 - - + -
229C PRO* 3.4 21.5 - - + +
239D TYR* 4.9 2.8 + - - -
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Residues in contact with LEU 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ASP* 4.0 16.4 - - + +
82A TYR* 4.5 1.6 - - + -
83A ILE* 4.2 28.0 - - + -
163A PHE* 5.0 0.4 - - + -
188A PHE 3.5 5.6 - - - +
189A LEU* 3.7 31.0 - - + -
211A GLU 3.6 1.0 - - - +
212A VAL* 3.1 6.1 - - - +
213A VAL* 2.9 43.6 + - + +
214A GLU* 5.5 0.4 - - - -
215A ILE* 3.7 32.8 - - + -
238A ALA 4.3 6.1 - - - +
239A TYR* 1.3 78.7 - - - +
241A VAL* 1.3 60.8 + - - +
242A PHE* 3.8 22.8 + - + -
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLY* 3.1 4.9 - - - -
188A PHE* 2.7 51.8 + - + +
190A LEU* 4.1 23.8 - - + -
196A VAL* 4.2 17.5 - - + -
199A LEU* 4.0 15.5 - - + -
200A LEU* 4.6 13.0 - - + -
203A ILE* 4.9 7.6 - - + -
210A LEU* 5.1 2.2 - - + -
211A GLU 3.3 7.9 - - - +
212A VAL* 4.1 19.1 - - + -
239A TYR 4.7 1.6 - - - +
240A LEU* 1.3 78.1 - - - +
242A PHE* 1.3 69.0 + - - +
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Residues in contact with PHE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 3.8 23.6 - + - -
83A ILE* 3.9 32.5 - - + -
86A LYS* 3.7 44.6 - - + -
87A LEU* 4.3 14.4 - - + -
163A PHE* 4.6 1.8 - + - -
185A PRO* 6.3 0.2 - - + -
186A VAL* 3.3 13.9 - - - +
187A GLY* 3.8 14.6 - - - -
188A PHE* 5.8 0.4 - - - -
203A ILE* 6.2 0.2 - - - -
209A ASN 3.8 1.3 - - - +
210A LEU* 3.3 8.5 - - - +
211A GLU* 2.7 44.2 + - + +
213A VAL* 4.2 8.5 - - + -
240A LEU* 3.8 26.2 - - + -
241A VAL* 1.3 76.6 - - - +
243A GLY* 1.3 59.4 + - - +
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Residues in contact with GLY 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A PRO* 3.4 5.4 - - - +
186A VAL* 3.0 39.5 + - - +
188A PHE* 5.6 0.2 - - - -
203A ILE* 5.8 0.4 - - - -
207A PHE* 4.4 2.0 - - - -
208A GLY 3.2 12.3 - - - -
209A ASN 3.8 4.0 - - - -
210A LEU* 4.1 8.5 - - - -
242A PHE* 1.3 76.2 - - - +
244A ARG* 1.3 67.3 + - - -
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Residues in contact with ARG 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLY 2.8 26.6 + - - -
184A ALA 3.6 2.7 - - - -
185A PRO* 3.7 23.0 - - - +
207A PHE* 3.3 5.5 - - - +
208A GLY* 2.8 30.5 + - - +
209A ASN* 3.8 23.8 - - + +
243A GLY* 1.3 82.8 - - - -
245A LYS* 1.3 64.2 + - - +
246A LEU 3.2 0.2 + - - -
11B LEU* 5.2 0.2 - - - +
46B GLU* 3.5 12.1 + - - -
56B TYR* 3.4 37.3 + - + +
57B ARG* 2.7 29.3 + - - +
59B THR* 3.7 17.4 - - - +
62B GLU* 3.5 22.6 + - - -
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A GLY* 5.5 0.2 - - - -
177A HIS* 2.8 54.4 + - + +
178A LYS* 4.4 5.7 + - - +
180A LEU* 2.6 27.6 + - + +
181A MET 3.4 15.5 - - - +
182A GLU* 3.0 33.1 + - - +
183A GLY* 3.4 20.8 + - - +
184A ALA 2.9 18.6 + - - +
207A PHE* 3.6 16.4 - - + -
244A ARG* 1.3 71.4 - - - +
246A LEU* 1.3 62.8 + - - +
248A THR 6.0 0.2 - - - +
47B GLY* 3.3 18.9 - - - -
56B TYR* 3.5 1.4 - - - -
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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