Contacts of the strand formed by residues 224 - 229 (chain A) in PDB entry 1LEC
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 ASP 224 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 3.7 23.7 + - - +
48A ARG* 5.3 4.4 + - - +
82A ASN* 3.6 0.2 - - - -
83A TYR* 2.8 49.3 + - + +
84A GLY* 5.2 1.6 - - - -
86A PRO 5.0 1.0 - - - +
87A THR* 3.4 13.6 - - + +
223A TYR* 1.3 98.0 - - + +
225A GLU* 1.3 59.6 + - - +
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Residues in contact with GLU 225 (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 THR* 4.0 2.8 + - - -
46A PRO* 3.2 19.5 - - - +
80A LEU* 3.5 22.7 - - + +
81A LYS 3.3 12.1 - - - +
82A ASN* 4.5 1.3 - - - +
87A THR* 2.8 26.8 + - - +
88A ALA 3.0 28.7 - - - +
89A ASP 3.4 1.8 + - - -
90A GLY* 3.0 25.5 + - - +
132A THR* 3.0 20.6 + - - +
221A VAL* 3.5 22.1 - - + +
223A TYR 3.1 3.6 + - - +
224A ASP* 1.3 80.6 - - - +
226A VAL* 1.3 62.4 + - - +
227A THR* 4.7 0.9 + - - -
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Residues in contact with VAL 226 (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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36A GLN* 4.0 15.9 - - + -
38A THR* 3.9 24.2 - - - +
40A THR* 3.7 29.6 - - + -
44A GLY 4.2 5.2 - - - +
46A PRO* 4.0 10.8 - - + -
79A LEU 3.4 1.6 - - - +
80A LEU* 3.5 2.1 - - - -
81A LYS* 2.8 44.3 + - + +
221A VAL* 5.4 0.7 - - - -
225A GLU* 1.3 80.8 - - - +
227A THR* 1.3 67.2 + - - +
228A TYR* 3.8 26.7 + - + +
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Residues in contact with THR 227 (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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36A GLN* 3.7 2.9 - - - -
37A LEU* 3.1 55.0 + - + +
38A THR* 4.7 2.6 + - - -
78A PHE* 4.4 7.2 - - + -
79A LEU 3.4 5.8 - - - +
80A LEU* 3.1 22.2 - - - +
90A GLY 4.6 2.8 + - - -
91A LEU* 3.7 29.1 - - + +
219A ALA* 4.9 2.7 - - - +
225A GLU* 4.7 0.9 + - - -
226A VAL* 1.3 75.4 - - - +
228A TYR* 1.3 67.6 + - - +
229A ILE* 4.0 15.3 - - + -
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Residues in contact with TYR 228 (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 ILE* 3.5 32.8 - - + -
34A ALA* 4.0 15.7 - - + -
35A LEU 3.4 2.7 - - - -
36A GLN* 3.7 23.2 + - + -
40A THR* 4.3 4.7 - - - +
44A GLY* 3.8 17.8 + - - -
78A PHE* 3.3 5.2 - - - +
79A LEU* 2.8 60.6 + - + +
81A LYS* 4.1 12.1 - - + +
226A VAL* 3.8 31.4 - - + +
227A THR* 1.3 74.8 - - - +
229A ILE* 1.3 60.4 + - - +
230A LEU* 3.7 10.4 + - + +
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Residues in contact with ILE 229 (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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11A PHE* 3.4 13.2 - - + -
34A ALA* 3.3 7.6 - - - -
35A LEU* 2.8 44.7 + - + +
37A LEU* 4.0 19.7 - - + -
76A PHE* 4.5 2.0 - - + -
77A THR 3.7 5.2 - - - +
78A PHE* 3.8 19.5 - - + -
91A LEU* 4.4 4.9 - - + -
217A PHE* 3.9 52.0 - - + -
227A THR* 4.0 15.3 - - + -
228A TYR* 1.3 71.0 - - - +
230A LEU* 1.3 59.3 + - - +
231A SER 3.5 22.9 - - - +
232A TRP* 4.8 0.2 - - + -
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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