Contacts of the strand formed by residues 218 - 223 (chain A) in PDB entry 1VCO
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 218 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A LEU* 3.7 33.2 - - + -
182A TYR 3.1 3.9 + - - +
183A LEU* 3.2 30.1 - - + -
184A HIS 3.0 23.6 + - - -
216A PRO* 3.9 1.2 - - - +
217A ASP* 1.3 86.2 - - + +
219A LEU* 1.3 72.1 + - - +
220A VAL* 4.5 0.4 - - + -
241A VAL* 4.2 0.7 - - - -
245A HIS* 3.4 27.1 - - + +
247A PHE* 3.8 19.1 - - + -
267A LEU* 4.1 6.1 - - + -
270A ALA* 4.6 7.4 - - + +
271A VAL* 4.0 24.9 - - + +
274A ALA* 5.1 1.1 - - + -
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Residues in contact with LEU 219 (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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184A HIS* 3.4 27.8 - - + +
186A THR* 5.6 1.1 - - + -
202A THR* 4.7 4.7 - - + -
206A VAL* 4.0 12.3 - - + -
216A PRO* 3.8 16.6 - - + -
218A ILE* 1.3 82.1 - - - +
220A VAL* 1.3 66.9 + - - +
221A LEU* 4.6 5.6 - - + -
235A VAL* 3.9 21.3 - - + -
239A THR* 3.5 31.9 - - + +
241A VAL* 3.7 15.5 - - + -
245A HIS 3.0 9.6 + - - +
246A VAL* 3.5 13.1 - - + -
247A PHE* 2.8 27.8 + - - -
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Residues in contact with VAL 220 (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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30A LEU* 4.2 18.4 - - + -
183A LEU* 3.8 31.9 - - + -
184A HIS 3.0 7.7 + - - +
185A LEU* 3.3 27.0 - - + +
186A THR* 3.0 25.8 + - - -
218A ILE* 4.5 3.8 - - + -
219A LEU* 1.3 78.7 - - - +
221A LEU* 1.3 62.5 + - - +
247A PHE* 3.3 12.1 - - + +
248A SER 4.2 10.3 - - - +
249A SER* 3.6 20.6 - - - -
262A LEU* 4.9 3.4 - - + -
267A LEU* 5.1 5.2 - - + -
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Residues in contact with LEU 221 (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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186A THR* 3.6 21.1 - - - +
188A VAL* 3.7 16.8 - - + -
202A THR* 4.0 20.6 - - + +
219A LEU* 4.6 7.0 - - + -
220A VAL* 1.3 74.1 - - - +
222A ARG* 1.3 63.2 + - - +
223A SER* 3.6 1.6 + - - -
227A VAL* 3.8 37.3 - - + +
231A VAL* 5.6 0.2 - - + -
232A ARG* 4.4 3.4 - - + -
235A VAL* 4.3 20.6 - - + -
246A VAL* 3.8 23.8 - - + -
247A PHE 2.8 17.4 + - - +
248A SER* 3.6 3.6 - - - -
249A SER* 2.9 24.2 + - - -
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Residues in contact with ARG 222 (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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25A LEU* 3.1 49.3 + - + +
26A GLY* 5.4 0.6 - - - -
185A LEU* 4.3 9.2 - - + -
186A THR 2.7 18.0 + - - +
187A LEU* 3.6 8.2 - - + +
188A VAL 2.8 29.3 + - - +
220A VAL 3.7 1.8 + - - -
221A LEU* 1.3 69.1 - - - +
223A SER* 1.3 83.1 + - - +
249A SER* 3.0 38.5 + - - -
250A PRO 4.3 1.6 - - - -
251A THR* 3.3 38.3 - - - +
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Residues in contact with SER 223 (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 LEU* 5.0 4.0 - - - -
188A VAL* 2.7 27.6 + - - -
190A TYR* 3.8 15.6 - - - +
197A PHE* 3.8 5.7 - - - -
221A LEU 3.6 1.2 + - - -
222A ARG* 1.3 96.9 + - - +
224A ALA* 1.3 72.4 + - - +
225A ARG 3.2 16.8 + - - -
227A VAL* 4.3 11.0 - - - -
249A SER 3.3 5.5 + - - -
250A PRO* 3.3 10.0 - - - +
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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