Contacts of the strand formed by residues 27 - 34 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ILE* 6.0 0.4 - - - -
25A ILE* 3.2 14.4 - - - +
26A PRO* 1.3 76.7 - - - +
28A MET* 1.3 61.9 + - - +
43A TRP 3.3 11.2 - - - -
44A GLY* 4.2 0.2 - - - -
45A TYR 3.4 12.3 - - - -
54A VAL* 3.7 6.7 - - - -
60A PHE* 4.6 1.3 - - - -
340A ALA* 3.4 0.5 - - - -
341A ASN* 2.8 33.2 + - - +
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Residues in contact with MET 28 (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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16A ILE* 4.1 15.9 - - + -
19A LEU* 4.0 6.5 - - + -
20A ILE* 4.2 11.0 - - + -
25A ILE* 4.0 25.8 - - + -
27A GLY* 1.3 77.4 - - - +
29A ALA* 1.3 66.1 + - - +
30A VAL* 4.3 14.4 - - + -
42A THR* 3.4 2.4 - - - -
43A TRP* 2.8 49.4 + - + +
54A VAL* 3.7 7.5 - - - +
60A PHE* 4.4 1.1 - - - -
338A MET* 3.6 35.0 - - + -
339A LEU 3.3 10.3 - - - +
340A ALA* 4.3 7.0 - - + -
344A TYR* 3.5 23.8 - - + +
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Residues in contact with ALA 29 (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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28A MET* 1.3 74.9 - - - +
30A VAL* 1.3 65.3 + - - +
41A PHE 3.3 9.0 - - - +
42A THR* 4.2 4.9 - - + +
54A VAL* 4.0 8.5 - - + -
55A THR 4.9 0.7 - - - +
60A PHE* 3.9 22.8 - - + -
227A ILE* 3.6 29.3 - - + +
339A LEU* 2.9 33.1 + - + +
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Residues in contact with VAL 30 (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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12A VAL* 4.5 11.0 - - + -
16A ILE* 4.1 19.3 - - + -
28A MET* 4.3 7.9 - - + -
29A ALA* 1.3 81.8 - - - +
31A ALA* 1.3 72.3 + - - +
32A VAL* 4.3 8.7 - - + -
39A TYR 4.4 0.2 - - - -
40A TYR* 3.4 2.6 - - - -
41A PHE* 2.8 41.8 + - + -
43A TRP* 3.4 29.6 - - + -
227A ILE* 3.8 5.3 - - - +
336A ILE* 4.1 17.9 - - + -
337A VAL 3.3 12.8 - - - +
338A MET* 4.3 7.4 - - + -
356A ILE* 5.2 0.2 - - + -
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Residues in contact with ALA 31 (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 VAL* 1.3 74.7 - - - +
32A VAL* 1.3 62.2 - - - +
33A ILE* 4.2 3.9 - - + +
39A TYR 3.2 6.5 - - - +
40A TYR* 3.8 14.6 - - + -
227A ILE* 3.6 22.0 - - + +
231A ALA* 3.9 21.5 - - + -
336A ILE* 3.2 7.1 - - - +
337A VAL* 2.9 36.8 + - + -
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Residues in contact with VAL 32 (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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8A ILE* 4.4 12.8 - - + -
12A VAL* 3.8 28.5 - - + -
30A VAL* 4.3 10.1 - - + -
31A ALA* 1.3 77.9 - - - +
33A ILE* 1.3 72.5 + - - +
34A TYR* 4.5 4.3 - - + +
37A LYS 3.5 2.1 - - - +
38A PRO* 3.4 0.9 - - - +
39A TYR* 2.9 36.3 + - + +
41A PHE* 4.5 2.5 - - + -
334A LEU* 4.6 1.6 - - + -
335A GLY 3.4 7.9 - - - +
336A ILE* 4.3 5.2 - - + -
356A ILE* 4.1 14.1 - - + -
357A LEU* 5.0 0.9 - - + -
360A LEU* 3.6 28.9 - - + -
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Residues in contact with ILE 33 (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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31A ALA* 4.3 7.4 - - + +
32A VAL* 1.3 79.1 - - - +
34A TYR* 1.3 59.9 + - - +
36A GLY* 3.9 23.8 - - - +
37A LYS 3.3 5.2 - - - +
38A PRO* 4.6 5.8 - - + -
231A ALA* 4.1 39.9 - - + +
234A VAL* 4.2 17.7 - - + -
235A GLN* 4.2 10.1 - - + -
238A LEU* 3.6 24.2 - - + -
333A GLU 3.9 6.1 - - - +
334A LEU* 3.3 11.6 - - - +
335A GLY* 2.8 40.8 + - - +
336A ILE* 4.7 0.7 - - - +
337A VAL* 5.1 0.4 - - + -
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Residues in contact with TYR 34 (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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5A PRO* 5.2 9.2 - - + -
7A GLN* 4.7 11.2 + - - -
8A ILE* 3.7 31.6 - - + -
32A VAL* 3.7 4.6 + - + -
33A ILE* 1.3 73.2 - - - +
35A GLN* 1.3 105.9 + - + +
36A GLY 3.0 0.7 - - - -
37A LYS* 2.8 26.0 + - - +
39A TYR* 3.9 13.8 + + + -
333A GLU 4.2 0.2 - - - -
334A LEU* 4.2 15.9 - - + -
360A LEU* 3.8 37.6 + - + -
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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