Contacts of the strand formed by residues 141 - 146 (chain D) in PDB entry 4IBU
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 CYS 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123D THR 5.2 0.2 - - - -
124D CYS* 3.7 11.4 - - - -
133D MET* 3.9 13.0 - - + -
135D CYS* 3.4 41.5 - - - -
136D GLN 5.0 0.9 - - - -
139D LYS 3.5 14.8 - - - -
140D THR* 1.3 76.6 - - - +
142D PRO* 1.3 68.2 - - - +
143D VAL* 3.5 4.0 + - + +
232D ILE 3.6 0.2 - - - +
234D TYR* 2.7 46.6 + - + +
236D TYR* 3.9 10.1 - - + -
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Residues in contact with PRO 142 (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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112D GLY 4.7 1.0 - - - +
113D PHE* 4.2 11.4 - - - +
114D LEU* 3.7 33.5 + - + +
124D CYS* 4.1 12.9 - - + -
133D MET* 4.1 7.8 - - - +
140D THR* 3.6 13.5 - - + +
141D CYS* 1.3 85.0 - - - +
143D VAL* 1.3 64.2 + - - +
144D GLN* 5.6 2.2 - - + -
231D THR* 4.0 5.6 - - + -
232D ILE 3.5 6.1 - - - +
233D HIS* 4.0 3.6 - - + -
305D EDO 3.5 32.1 - - - +
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Residues in contact with VAL 143 (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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111D LEU* 3.9 26.9 - - + -
112D GLY 4.0 2.7 - - - +
113D PHE* 4.1 11.9 - - + -
133D MET* 3.9 20.9 - - + -
141D CYS 4.1 1.6 - - - +
142D PRO* 1.3 81.0 - - - +
144D GLN* 1.3 64.8 + - - +
145D LEU* 4.0 5.5 + - + +
230D THR 3.7 0.5 - - - +
231D THR* 3.5 1.5 - - - +
232D ILE* 2.9 35.4 + - - +
234D TYR* 3.7 35.4 - - + -
236D TYR* 6.4 0.2 - - + -
255D ILE* 4.8 2.5 - - + -
270D PHE* 4.0 17.3 - - + -
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Residues in contact with GLN 144 (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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111D LEU* 3.3 13.2 - - - +
112D GLY* 2.8 48.0 + - - +
113D PHE* 3.8 7.7 + - - +
114D LEU* 3.5 35.1 - - + +
142D PRO 5.6 1.3 - - - -
143D VAL* 1.3 74.4 - - - +
145D LEU* 1.3 61.4 + - - +
146D TRP* 2.9 33.4 + - - +
229D CYS* 3.6 22.8 - - - -
230D THR 3.3 4.0 - - - -
231D THR* 3.8 14.1 + - + +
305D EDO 5.3 1.2 + - - -
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Residues in contact with LEU 145 (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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109D PHE* 3.8 22.0 - - + -
110D ARG 3.7 2.9 - - - -
111D LEU* 3.8 22.9 - - + -
143D VAL* 4.7 7.0 - - + +
144D GLN* 1.3 74.5 - - - +
146D TRP* 1.3 61.0 + - - +
147D VAL* 4.2 1.9 - - + +
157D VAL* 3.8 37.7 - - + -
220D TYR* 4.0 21.2 + - + -
223D PRO* 5.3 0.9 - - - +
229D CYS* 3.3 5.5 - - - +
230D THR* 2.6 51.7 + - + +
232D ILE* 3.8 19.1 - - + -
234D TYR* 6.3 0.2 - - + -
255D ILE* 4.2 3.6 - - + -
257D LEU* 5.1 0.2 - - + -
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Residues in contact with TRP 146 (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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108D GLY 3.3 2.9 - - - +
109D PHE* 3.4 0.7 - - - -
110D ARG* 2.8 70.9 + - - +
111D LEU 4.2 2.5 - - - -
112D GLY* 3.7 23.8 - - - -
144D GLN* 2.9 31.3 + - + +
145D LEU* 1.3 77.9 - - - +
147D VAL* 1.3 67.5 + - - +
228D ASP* 3.7 40.4 - - + -
229D CYS* 3.4 22.4 - - + +
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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