Contacts of the strand formed by residues 27 - 34 (chain B) in PDB entry 1LL9
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 GLY 27 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 5.7 0.4 - - - -
25B ILE* 3.2 7.3 - - - +
26B PRO* 1.3 76.7 - - - +
28B MET* 1.3 64.7 + - - +
43B TRP* 3.5 11.0 - - - -
45B TYR 3.3 15.9 - - - -
54B VAL* 3.7 5.2 - - - -
60B PHE* 4.6 1.6 - - - -
340B ALA* 3.4 0.2 - - - -
341B ASN* 2.8 36.1 + - - +
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Residues in contact with MET 28 (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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16B ILE* 3.9 9.4 - - + -
19B LEU* 4.3 3.8 - - + -
20B ILE* 3.8 38.6 - - + -
25B ILE* 4.1 15.5 - - + -
27B GLY* 1.3 76.6 - - - +
29B ALA* 1.3 70.3 + - - +
30B VAL* 4.3 9.4 - - + -
42B THR* 3.4 2.4 - - - -
43B TRP* 2.9 37.3 + - + +
54B VAL* 3.7 7.8 - - - +
60B PHE* 4.4 1.8 - - - -
338B MET* 3.8 33.9 - - + -
339B LEU 3.2 11.4 - - - +
340B ALA* 4.2 8.7 - - + -
344B TYR* 3.3 26.5 - - - +
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Residues in contact with ALA 29 (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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28B MET* 1.3 74.5 - - - +
30B VAL* 1.3 66.8 + - - +
41B PHE 3.3 7.2 - - - +
42B THR* 4.4 2.5 - - + -
54B VAL* 3.9 17.5 - - + -
55B THR 5.0 0.7 - - - +
60B PHE* 4.0 13.6 - - + -
227B ILE* 3.6 33.0 - - + +
339B LEU* 2.8 32.9 + - + +
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Residues in contact with VAL 30 (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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12B VAL* 4.8 6.7 - - + -
16B ILE* 4.2 17.7 - - + -
28B MET* 4.3 7.9 - - + -
29B ALA* 1.3 79.7 - - - +
31B ALA* 1.3 72.5 + - - +
32B VAL* 4.2 4.9 - - + -
40B TYR* 3.5 2.6 - - - -
41B PHE* 2.8 45.6 + - + +
43B TRP* 3.7 24.7 - - + -
227B ILE* 3.8 5.0 - - - +
336B ILE* 4.1 17.5 - - + -
337B VAL 3.2 13.7 - - - +
338B MET* 4.1 13.7 - - + -
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Residues in contact with ALA 31 (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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30B VAL* 1.3 75.0 - - - +
32B VAL* 1.3 62.9 + - - +
33B ILE* 4.4 2.8 - - + +
39B TYR 3.2 6.5 - - - +
40B TYR* 3.9 9.0 - - + -
227B ILE* 3.7 21.3 - - + +
231B ALA* 3.8 27.6 - - + -
336B ILE* 3.3 7.3 - - - +
337B VAL* 2.9 36.7 + - + -
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Residues in contact with VAL 32 (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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8B ILE* 4.3 12.1 - - + -
12B VAL* 4.0 16.6 - - + -
30B VAL* 4.2 8.5 - - + -
31B ALA* 1.3 78.6 - - - +
33B ILE* 1.3 72.7 + - - +
34B TYR* 4.5 1.8 - - + +
37B LYS 3.4 3.8 - - - +
38B PRO* 3.4 0.2 - - - +
39B TYR* 2.9 33.6 + - + -
41B PHE* 4.0 22.2 - - + -
335B GLY 3.4 8.3 - - - +
336B ILE* 4.2 9.4 - - + -
356B ILE* 4.3 9.2 - - + -
357B LEU* 4.9 2.7 - - + -
360B LEU* 3.8 27.4 - - + -
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Residues in contact with ILE 33 (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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31B ALA* 4.4 5.8 - - + +
32B VAL* 1.3 79.8 - - - +
34B TYR* 1.3 60.6 + - - +
36B GLY* 3.6 32.5 - - - +
37B LYS 3.2 4.7 - - - +
38B PRO* 4.6 6.3 - - + -
231B ALA* 4.2 19.5 - - + +
234B VAL* 4.0 26.0 - - + -
235B GLN* 4.1 20.6 - - + -
238B LEU* 3.7 20.2 - - + -
333B GLU 3.8 2.2 - - - +
334B LEU* 3.3 12.1 - - - +
335B GLY 2.8 42.2 + - - +
336B ILE* 4.6 0.7 - - - +
337B VAL* 4.9 0.9 - - + -
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Residues in contact with TYR 34 (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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5B PRO* 5.3 9.2 - - + -
7B GLN* 3.6 20.5 + - - -
8B ILE* 3.4 33.9 - - + -
32B VAL* 3.7 2.8 + - + -
33B ILE* 1.3 72.2 - - - +
35B GLN* 1.3 112.6 + - + +
36B GLY 3.1 0.4 - - - -
37B LYS* 2.8 25.4 + - - +
39B TYR* 3.8 13.2 + + + -
333B GLU 4.1 0.4 - - - -
334B LEU* 3.9 16.6 - - + -
360B LEU* 3.8 33.6 + - + -
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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