Contacts of the strand formed by residues 95 - 98 (chain D) in PDB entry 4WLE
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 95 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25D ALA* 5.5 0.4 - - + -
26D LYS 3.3 3.8 + - - +
27D VAL* 3.3 15.6 - - + +
28D ALA 2.9 24.1 + - - -
93D CYS* 4.1 0.9 - - - +
94D ASP* 1.3 87.0 - - + +
96D VAL* 1.3 67.4 + - - +
97D VAL* 4.1 15.5 - - + -
136D MET* 3.5 14.4 - - + +
138D CYS* 4.1 22.7 - - - -
259D VAL* 4.6 9.9 - - + -
262D LEU* 4.5 5.8 - - + -
263D VAL* 4.1 18.2 - - + -
266D MET* 4.0 24.2 - - + -
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Residues in contact with VAL 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ALA* 3.6 6.5 - - + +
30D LEU* 3.6 37.0 - - + -
90D LEU* 4.1 9.0 - - + -
93D CYS* 4.3 6.1 - - + -
95D VAL* 1.3 78.1 - - - +
97D VAL* 1.3 59.6 + - - +
98D ILE* 4.1 7.6 - - + +
128D CYS* 3.8 8.5 - - - -
132D CYS* 3.7 29.6 - - - -
135D ALA* 4.1 9.9 - - + -
136D MET 2.7 12.4 + - - +
137D ILE* 3.6 10.9 - - + +
138D CYS* 2.8 32.7 + - - +
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Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D VAL* 4.0 21.3 - - + -
28D ALA 2.9 7.5 + - - +
29D VAL* 3.5 4.9 - - + -
30D LEU* 2.9 25.5 + - - +
40D LEU* 3.8 17.9 - - + -
44D LEU* 4.8 4.5 - - + -
95D VAL* 4.1 5.6 - - + -
96D VAL* 1.3 76.6 - - - +
98D ILE* 1.3 64.5 + - - +
99D PRO* 3.2 5.3 - - + +
138D CYS* 3.4 13.0 - - + +
140D ILE* 3.8 26.2 - - + -
169D VAL* 5.6 0.4 - - + -
255D GLY* 5.4 1.3 - - - +
259D VAL* 3.4 33.4 - - + -
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Residues in contact with ILE 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 3.7 29.6 - - + +
96D VAL* 4.1 8.7 - - + +
97D VAL* 1.3 78.3 - - - +
99D PRO* 1.3 57.2 - - - +
100D ALA* 3.2 9.4 + - + +
120D ILE* 5.6 0.2 - - + -
121D VAL* 5.1 8.3 - - + -
124D LEU* 3.8 28.3 - - + -
125D THR* 3.9 27.6 - - + -
128D CYS* 4.7 2.7 - - - -
137D ILE* 4.3 14.8 - - + -
138D CYS 2.9 15.3 + - - +
139D VAL* 4.4 9.2 - - + -
140D ILE* 3.0 22.0 + - - -
141D ALA* 3.2 13.2 + - + -
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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