Contacts of the strand formed by residues 32 - 37 (chain L) in PDB entry 1LP9
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 LEU 32 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3L VAL* 4.7 1.1 - - + -
22L CYS* 4.3 1.8 - - - -
24L TYR* 3.8 39.5 - - + -
30L PRO* 3.6 18.6 - - + -
31L PHE* 1.3 79.7 - - - +
33L PHE* 1.3 69.1 + - - +
49L SER* 2.8 37.9 + - - -
66L LEU* 4.5 5.2 - - + -
73L PHE* 3.5 24.5 - - + -
90L CYS* 3.9 21.3 - - - -
91L ALA 3.2 16.8 - - - +
92L LEU* 3.5 21.1 - - + -
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Residues in contact with PHE 33 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31L PHE* 3.8 10.3 - - + -
32L LEU* 1.3 85.4 - - - +
34L TRP* 1.3 63.9 + - - +
35L TYR* 4.1 10.8 - - + -
45L LEU* 4.0 16.8 - - + -
47L LEU 3.3 9.0 - - - +
48L LYS* 3.6 32.3 - - + -
49L SER 5.2 0.4 - - - -
50L PHE* 3.8 18.2 - + - -
73L PHE* 4.3 1.1 - - - -
89L TYR 3.7 0.3 - - - +
90L CYS* 3.5 5.2 - - - -
91L ALA* 2.7 43.3 + - + +
93L PHE* 3.4 30.3 - - + -
104L LEU* 4.1 8.1 - - + -
100M TYR* 3.4 42.6 - + + -
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Residues in contact with TRP 34 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L GLN* 3.5 24.9 - - - -
20L LEU* 3.7 17.0 - - + -
21L ASN 4.3 2.7 - - - -
22L CYS* 3.6 15.3 - - + -
33L PHE* 1.3 73.9 - - - +
35L TYR* 1.3 61.7 + - - +
45L LEU* 3.6 4.5 - - - +
46L LEU* 2.9 33.6 + - + -
47L LEU* 3.0 34.1 + - + +
64L ALA* 4.0 6.0 - - + +
73L PHE* 2.9 57.7 + + - -
75L LEU* 3.5 44.5 - - + +
88L TYR* 3.8 22.0 - - + -
89L TYR 3.2 21.5 - - - -
90L CYS* 3.8 10.5 - - + -
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Residues in contact with TYR 35 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33L PHE* 4.1 11.9 - - + -
34L TRP* 1.3 80.0 - - - +
36L VAL* 1.3 61.5 + - - +
43L PRO* 4.5 3.8 - - + -
44L LYS* 3.3 26.9 - - - +
45L LEU* 3.5 29.6 - - + -
46L LEU* 4.2 1.6 - - - +
88L TYR* 3.5 5.6 - - - +
89L TYR* 2.8 49.0 + - + +
91L ALA* 4.7 1.8 - - + -
104L LEU* 3.5 22.4 - - + +
106L PHE* 3.8 16.6 - + + -
100M TYR 2.6 24.2 + - - -
105M GLU* 3.4 2.6 - - - -
106M GLN 2.9 33.9 + - - -
108M PHE* 3.7 18.2 - + - -
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Residues in contact with VAL 36 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L TYR* 1.3 75.0 - - - +
37L GLN* 1.3 63.8 + - - +
38L HIS* 4.1 12.9 + - + +
42L ALA 3.9 0.5 - - - +
43L PRO* 3.3 1.6 - - - +
44L LYS* 2.8 66.9 + - + +
46L LEU* 4.3 21.5 - - + -
86L ALA* 3.7 20.4 - - + -
87L LEU 3.5 4.0 - - - +
88L TYR* 3.4 33.9 - - + +
89L TYR* 5.5 0.4 - - - -
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Residues in contact with GLN 37 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L VAL* 1.3 73.6 - - - +
38L HIS* 1.3 68.3 + - - +
39L LEU* 4.0 0.8 + - - -
40L ASN* 5.1 3.2 - - - +
41L GLU 3.0 30.7 + - - +
42L ALA 4.3 1.3 - - - -
43L PRO* 3.9 22.7 - - + -
86L ALA* 3.5 2.8 - - - +
87L LEU* 2.8 55.0 + - + +
89L TYR* 4.4 5.3 - - + -
37M GLN* 2.9 29.8 + - - +
91M PHE* 3.5 20.4 - - - -
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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