Contacts of the strand formed by residues 204 - 209 (chain B) in PDB entry 1L0N
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 MET 204 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B GLY 4.5 2.1 - - - +
33B LEU* 3.6 13.8 - - + -
34B VAL* 3.5 18.4 + - - +
49B LEU* 3.7 24.0 - - + -
50B PHE 3.3 4.3 - - - -
51B ILE* 4.0 22.9 - - + -
127B THR* 6.0 0.9 - - - +
128B THR* 5.6 2.5 - - + -
199B PHE* 3.6 26.5 - - - +
200B THR 3.2 24.9 - - - +
201B SER 3.0 6.5 + - - +
202B ALA 3.5 0.6 - - - -
203B ARG* 1.3 82.2 - - - +
205B ALA* 1.3 62.7 + - - +
224B LEU* 3.6 40.6 - - + +
226B ILE* 5.5 2.5 - - - -
387B LEU* 4.0 5.6 - - - +
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Residues in contact with ALA 205 (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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33B LEU* 4.8 0.4 - - - -
34B VAL* 3.5 11.9 - - + +
48B GLY 3.6 1.7 - - - +
49B LEU* 3.4 5.8 - - - +
50B PHE* 2.7 46.7 + - + +
204B MET* 1.3 77.8 - - - +
206B LEU* 1.3 59.5 + - - +
207B ILE* 3.8 5.3 + - + -
386B ALA* 3.8 22.2 - - + -
387B LEU* 3.6 20.0 - - + -
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Residues in contact with LEU 206 (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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33B LEU* 5.0 1.9 - - + +
34B VAL 3.1 11.8 + - - +
35B ILE* 3.5 13.0 - - + +
36B ALA 3.2 19.8 + - - +
47B ILE* 4.1 23.1 - - + -
48B GLY 3.8 3.8 - - - +
49B LEU* 3.9 19.1 - - + -
120B MET* 5.0 4.9 - - - -
123B LEU* 4.5 11.7 - - + -
124B LEU* 5.4 2.0 - - + -
205B ALA* 1.3 70.1 - - - +
207B ILE* 1.3 60.6 + - - +
216B LEU* 3.7 44.3 - - + +
219B VAL* 3.9 16.8 - - + -
220B ALA* 4.1 6.3 - - + -
224B LEU* 4.0 17.9 - - + -
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Residues in contact with ILE 207 (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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34B VAL* 5.1 0.7 - - + -
35B ILE 5.0 0.2 - - - -
36B ALA* 3.1 30.7 - - + +
47B ILE* 3.4 7.3 - - - +
48B GLY 2.9 32.9 + - - +
50B PHE* 3.7 28.0 - - + -
205B ALA* 4.3 5.4 - - + +
206B LEU* 1.3 78.2 - - - +
208B GLY* 1.3 64.4 + - - +
209B LEU* 5.4 1.8 - - + -
216B LEU* 4.0 2.0 - - - -
378B PHE* 6.1 0.4 - - + -
379B LEU* 3.7 23.7 - - + +
382B VAL* 4.0 28.5 - - + +
383B GLY* 3.8 13.0 - - - -
386B ALA* 4.4 12.1 - - + -
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Residues in contact with GLY 208 (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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36B ALA 2.8 11.9 + - - +
37B SER* 3.2 2.9 - - - -
38B LEU 3.0 24.9 + - - -
46B ARG 3.5 5.8 - - - -
47B ILE* 4.0 2.9 - - - -
207B ILE* 1.3 77.2 - - - +
209B LEU* 1.3 66.6 + - - +
210B GLY 4.1 0.2 - - - -
211B VAL* 3.8 13.0 - - - -
216B LEU* 3.5 15.9 - - - +
379B LEU* 4.4 1.3 - - - -
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Residues in contact with LEU 209 (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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38B LEU* 3.7 13.9 - - + +
40B ASN* 3.5 25.4 - - - +
44B ALA 4.9 0.7 - - - -
45B SER* 3.1 5.5 - - - -
46B ARG* 2.6 53.8 + - + +
207B ILE* 5.4 1.3 - - + -
208B GLY* 1.3 83.7 - - - +
210B GLY* 1.3 62.1 + - - +
211B VAL* 3.3 1.8 - - - +
375B SER* 3.7 36.6 - - - +
378B PHE* 3.6 35.7 - - + -
379B LEU* 3.8 12.6 - - + -
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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