Contacts of the strand formed by residues 178 - 184 (chain A) in PDB entry 1LEI
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 VAL 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TYR* 6.2 0.7 - - + -
21A VAL* 3.3 44.0 - - + +
23A ILE* 4.5 8.5 - - + -
160A CYS* 3.5 3.3 - - - -
161A PHE* 2.9 61.2 + - + +
176A THR* 3.6 13.0 - - + +
177A PRO* 1.3 79.9 - - - +
179A LEU* 1.3 63.9 + - - +
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Residues in contact with LEU 179 (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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23A ILE* 3.3 13.8 - - - +
26A GLN* 4.8 1.6 + - - -
77A VAL* 3.6 25.4 - - + -
83A HIS* 3.5 46.4 - - + +
141A PHE* 3.7 16.6 - - + -
158A ARG* 4.3 12.8 - - - +
159A LEU 3.4 7.0 - - - +
160A CYS* 3.7 23.3 - - - -
178A VAL* 1.3 77.1 - - - +
180A SER* 1.3 67.1 + - - +
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Residues in contact with SER 180 (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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23A ILE* 3.6 13.2 - - - +
26A GLN* 3.2 15.0 - - - -
27A PRO* 3.5 20.3 - - - +
158A ARG* 2.7 33.8 + - - +
159A LEU* 3.2 34.3 + - - +
161A PHE* 4.4 2.9 - - - -
179A LEU* 1.3 74.5 - - - +
181A HIS* 1.3 70.4 + - - +
183A ILE* 4.9 0.2 - - - +
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Residues in contact with HIS 181 (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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26A GLN* 2.6 53.3 + - + +
27A PRO* 4.3 2.9 - - + +
29A GLN* 3.6 31.3 + - + +
49A GLU* 3.9 12.6 + - - -
158A ARG* 4.2 4.2 - - - +
180A SER* 1.3 91.0 + - - +
182A PRO* 1.3 71.3 - - + +
183A ILE* 3.6 6.6 + - - +
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Residues in contact with PRO 182 (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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29A GLN* 2.9 49.0 + - - +
79A LYS* 4.2 26.2 - - + +
156A ALA* 5.0 1.6 - - + -
157A VAL 3.5 10.8 - - - +
158A ARG* 3.9 28.7 - - + +
181A HIS* 1.3 83.1 - - + +
183A ILE* 1.3 61.2 + - - +
184A PHE* 3.7 24.9 - - + -
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Residues in contact with ILE 183 (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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27A PRO* 3.4 37.7 - - + +
28A LYS 4.1 9.4 - - - +
29A GLN* 3.6 8.3 - - - +
32A MET* 5.7 8.3 - - + +
34A PHE* 3.8 16.2 - - + -
46A ILE* 3.8 26.7 - - + -
118A ILE* 4.4 11.2 - - + -
156A ALA* 3.4 3.5 - - - -
157A VAL* 2.9 39.6 + - + +
159A LEU* 3.9 14.8 - - + +
181A HIS 4.0 5.4 - - - +
182A PRO* 1.3 77.0 - - - +
184A PHE* 1.3 68.8 + - - +
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Residues in contact with PHE 184 (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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29A GLN* 2.7 33.3 + - + +
30A ARG* 3.3 40.4 - - + +
32A MET 3.3 11.3 - - - +
34A PHE* 3.9 5.1 - - - -
79A LYS* 4.5 15.3 - - + -
153A ASP* 5.7 0.2 - - - -
155A ASN 3.2 2.9 - - - -
156A ALA* 3.7 23.6 - - + -
182A PRO* 3.7 36.3 - - + -
183A ILE* 1.3 78.9 - - - +
185A ASP* 1.3 64.5 + - - +
186A ASN* 3.2 4.6 + - - -
191A THR* 3.4 42.8 - - + +
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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