Contacts of the strand formed by residues 206 - 209 (chain A) in PDB entry 4L1O
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 VAL 206 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A HIS* 3.8 3.6 - - - -
183A ILE* 3.2 19.1 - - + +
195A ILE* 4.5 6.5 - - + -
196A MET* 4.3 18.4 - - + -
199A ALA* 3.5 32.3 - - + -
204A THR 3.7 1.1 - - - +
205A PRO* 1.3 78.6 - - - +
207A THR* 1.3 64.4 + - - +
208A LEU* 3.9 28.8 + - + -
409A MET* 4.1 24.2 - - - +
410A GLY* 4.9 2.4 - - - -
196B MET* 4.7 4.9 - - + -
409B MET* 5.5 0.4 - - - -
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Residues in contact with THR 207 (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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182A HIS* 2.8 27.9 + - - -
183A ILE 2.8 7.8 + - - +
184A LEU* 3.2 28.2 - - + +
185A TYR 2.9 27.5 + - - +
206A VAL* 1.3 71.7 + - - +
208A LEU* 1.3 65.3 + - - +
209A GLU* 5.3 2.0 - - + +
409A MET 3.6 11.2 - - - +
410A GLY* 4.2 4.5 - - - -
411A SER* 4.0 24.7 - - - +
412A TYR* 4.6 4.9 - - + -
420A THR* 3.4 12.0 - - + +
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Residues in contact with LEU 208 (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 ILE 5.0 0.4 - - - +
185A TYR* 3.5 24.5 - - + -
192A GLY 3.8 17.0 - - - +
195A ILE* 4.1 17.0 - - + -
196A MET* 4.4 6.3 - - + +
206A VAL* 3.9 30.5 - - + -
207A THR* 1.3 81.5 - - - +
209A GLU* 1.3 59.8 + - - +
210A LEU* 3.8 16.6 - - + -
402A GLY* 5.8 0.3 - - - -
403A GLY 4.8 3.1 + - - -
407A SER 4.0 0.2 - - - +
408A GLY* 3.1 5.4 - - - -
409A MET* 3.0 47.7 + - + +
410A GLY 5.1 0.2 - - - +
203B LEU* 4.0 20.6 - - + -
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Residues in contact with GLU 209 (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 LEU* 5.9 1.1 - - + -
185A TYR 2.9 9.3 + - - +
186A THR* 3.3 25.4 + - - +
187A GLY 3.0 25.8 + - - +
207A THR* 4.1 2.6 - - + -
208A LEU* 1.3 71.4 - - - +
210A LEU* 1.3 72.5 + - - +
243A CYS* 3.8 6.4 - - - +
361A LEU* 3.6 17.8 - - + +
401A PHE* 3.5 29.6 - - + -
402A GLY* 5.2 5.4 - - - -
403A GLY 5.5 0.7 - - - +
407A SER 4.0 2.0 - - - -
412A TYR* 5.2 6.7 + - + -
601A 1VL 2.8 38.8 + - - -
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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