Contacts of the strand formed by residues 95 - 99 (chain A) in PDB entry 1L1G
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 ALA 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A VAL 3.8 0.2 - - - +
41A MET* 3.6 4.3 - - - +
42A THR* 2.9 36.5 + - + +
43A ALA 4.1 3.1 - - - +
44A ALA* 3.8 20.2 - - - +
47A VAL* 3.9 18.8 - - + -
77A ILE* 4.9 0.2 - - + -
78A VAL 3.3 12.8 - - - +
79A VAL* 4.0 6.3 - - + -
94A ILE* 1.3 78.7 - - - +
96A LEU* 1.3 65.1 + - - +
97A LEU* 4.7 3.4 - - + -
232A TRP* 4.2 2.5 - - - -
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Residues in contact with LEU 96 (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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35A ILE* 3.8 26.5 - - + -
39A TRP* 3.7 18.5 - - + -
40A VAL 3.3 2.9 - - - +
41A MET* 3.9 17.5 - - + -
76A LYS 3.9 0.3 - - - +
77A ILE* 3.7 1.9 - - - -
78A VAL* 2.8 41.4 + - - +
95A ALA* 1.3 81.2 - - - +
97A LEU* 1.3 62.9 + - - +
232A TRP* 3.7 18.8 - - + -
233A ILE* 3.8 25.4 - - + +
236A VAL* 3.6 33.4 - - + -
237A ILE* 4.4 6.7 - - + -
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Residues in contact with LEU 97 (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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18A LEU* 3.6 33.2 - - + -
39A TRP* 3.3 8.0 - - - -
40A VAL* 2.8 50.4 + - + +
42A THR* 3.9 27.4 - - + -
47A VAL* 4.2 7.2 - - + -
53A PHE* 5.7 0.4 - - + -
55A VAL* 4.2 7.6 - - + -
74A VAL* 4.1 21.8 - - + -
76A LYS 3.4 3.1 - - - -
77A ILE* 4.0 28.0 - - + -
95A ALA* 4.7 1.6 - - + -
96A LEU* 1.3 81.5 - - - +
98A ARG* 1.3 60.6 + - - +
99A LEU* 3.7 3.3 + - + +
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Residues in contact with ARG 98 (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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38A ASN* 3.3 24.0 - - - +
39A TRP* 3.7 25.7 - - + -
74A VAL* 3.8 1.9 - - - -
75A GLN* 2.6 63.5 + - - +
76A LYS* 2.8 44.5 + - + +
97A LEU* 1.3 71.7 - - - +
99A LEU* 1.3 67.0 + - - +
240A ASN* 3.1 44.9 + - - +
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Residues in contact with LEU 99 (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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34A LEU* 4.1 18.2 - - + -
37A GLN 3.8 20.4 - - - +
38A ASN* 2.8 29.0 + - - +
39A TRP 4.1 0.4 - - - +
40A VAL* 4.0 12.3 - - + -
55A VAL* 3.9 32.3 - - + -
72A VAL* 3.9 19.7 - - + -
73A GLY 3.6 8.3 - - - +
74A VAL* 4.5 4.7 - - + -
75A GLN* 3.8 5.5 - - - +
97A LEU 4.1 6.1 - - - +
98A ARG* 1.3 88.2 - - - +
100A ALA* 1.3 67.2 + - - +
101A GLN 3.2 16.1 + - - +
103A VAL* 4.3 4.0 - - + -
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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