Contacts of the strand formed by residues 153 - 158 (chain D) in PDB entry 4TUG
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 LYS 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121D PHE* 3.3 19.7 - - + +
144D GLU* 5.7 5.7 + - + +
147D ALA* 3.8 21.7 + - + +
148D LYS* 4.4 7.5 + - - +
150D TYR* 3.1 28.2 + - + +
151D LYS* 4.0 10.3 - - - +
152D LYS* 1.3 74.6 - - - +
154D ILE* 1.3 63.4 + - - +
178D LYS* 3.9 19.9 + - - +
179D PHE* 3.5 26.2 - - + +
180D SER* 2.6 52.5 + - - +
181D TYR 3.6 0.3 + - - -
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Residues in contact with ILE 154 (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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3D PHE* 4.1 17.9 - - + -
45D LEU* 3.8 19.1 - - + -
120D ILE* 3.6 26.0 - - + -
121D PHE 2.8 9.7 + - - +
122D ILE* 3.3 23.7 - - + +
123D CYS* 3.0 26.9 + - - +
153D LYS* 1.3 79.0 - - - +
155D LEU* 1.3 66.0 + - - +
156D MET* 5.1 0.4 - - + -
179D PHE* 4.2 2.7 - - - -
181D TYR* 3.3 35.9 - - + +
183D ALA* 4.5 0.7 - - + -
229D PHE* 3.9 25.1 - - + -
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Residues in contact with LEU 155 (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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123D CYS* 3.3 30.1 - - - +
140D LEU* 3.7 21.5 - - + -
143D PHE* 3.8 17.3 - - + -
154D ILE* 1.3 72.7 - - - +
156D MET* 1.3 65.6 + - - +
157D LEU* 3.7 17.7 + - + -
176D LEU* 4.5 7.2 - - + -
179D PHE* 3.5 39.6 - - + -
181D TYR 3.1 6.5 + - - -
182D TYR* 3.6 21.8 - - + -
183D ALA* 2.8 33.2 + - - +
184D LEU* 4.8 1.7 - - + +
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Residues in contact with MET 156 (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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45D LEU* 3.8 26.9 - - + -
46D HIS 3.1 47.1 - - - +
47D SER* 4.3 2.9 - - - +
79D TYR* 3.6 21.8 - - - +
80D ILE* 4.1 1.3 - - - -
81D VAL* 4.0 15.7 - - + +
107D LEU* 4.3 11.9 - - - -
122D ILE* 4.5 7.4 - - + -
123D CYS 2.8 15.7 + - - +
124D GLY* 3.0 24.3 - - - -
125D THR 3.4 4.2 + - - -
154D ILE* 5.1 0.2 - - + -
155D LEU* 1.3 71.8 - - - +
157D LEU* 1.3 68.0 + - - +
183D ALA* 3.3 21.5 - - + +
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Residues in contact with LEU 157 (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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47D SER* 3.9 3.3 - - - -
81D VAL* 4.5 5.8 - - - +
124D GLY 5.3 0.2 - - - -
125D THR* 3.7 32.3 - - + +
136D MET* 4.3 8.1 - - - -
140D LEU* 3.9 19.7 - - + -
143D PHE* 6.0 0.2 - - + -
155D LEU* 3.7 30.5 - - + -
156D MET* 1.3 83.2 - - - +
158D HIS* 1.3 59.3 + - - +
159D GLN* 3.7 24.7 - - + +
161D ILE* 5.8 1.3 - - + -
171D LEU* 4.7 5.8 - - + -
176D LEU* 4.5 16.4 - - + -
183D ALA 3.0 7.7 + - - +
184D LEU* 3.3 20.3 - - + +
185D GLY 3.0 21.0 + - - -
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Residues in contact with HIS 158 (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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8D ASP* 3.5 7.0 - - - -
47D SER 2.7 26.8 + - - +
48D GLY 3.7 3.5 - - - -
49D ASP* 2.9 31.7 + - + -
81D VAL* 4.6 3.3 - - + +
82D ALA 4.2 8.1 - - - +
83D GLY* 3.4 11.2 - - - -
84D ASN* 2.3 43.4 + - - -
125D THR 4.4 3.4 + - - -
127D TYR* 3.0 19.6 - + + +
157D LEU* 1.3 72.5 - - - +
159D GLN* 1.3 69.6 + - - +
185D GLY 3.4 4.3 - - - -
186D HIS* 3.1 29.6 + - + -
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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