Contacts of the helix formed by residues 141 - 146 (chain B) in PDB entry 1UW9
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 PRO 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ASP 3.3 25.8 - - - +
34B THR* 3.3 25.8 - - - +
35B ASP 3.6 9.2 - - - +
36B ILE* 3.7 21.8 - - + -
105B ILE* 4.8 0.2 - - + -
139B ARG* 3.3 18.1 - - - +
140B ILE* 1.3 87.8 - - + +
142B PRO* 1.3 72.0 - - + +
143B ALA 4.3 2.2 - - - +
144B TYR* 2.9 22.1 + - + +
145B VAL* 2.9 11.2 + - - +
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Residues in contact with PRO 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 4.6 5.8 - - - +
139B ARG* 5.5 2.7 - - - +
140B ILE 3.8 3.6 - - - +
141B PRO* 1.3 85.6 - - + +
143B ALA* 1.3 56.5 + - - +
145B VAL* 3.6 9.9 - - + +
146B LYS* 3.0 37.4 + - - +
367B ASP* 3.8 39.5 - - + +
369B SMC 3.9 26.9 - - + -
34O THR* 4.4 14.1 - - + -
143O ALA* 4.3 0.7 - - + -
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASP 5.6 0.2 + - - -
34B THR* 4.1 24.0 - - + -
105B ILE* 3.7 18.3 - - + +
141B PRO* 3.1 2.4 + - - +
142B PRO* 1.3 80.0 - - - +
144B TYR* 1.3 57.8 + - - +
146B LYS* 4.1 3.8 + - - +
147B THR* 3.6 5.2 - - - +
142O PRO* 4.3 4.7 - - + -
143O ALA* 3.7 32.4 - - + +
146O LYS* 3.4 26.2 - - + +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B ILE* 4.2 14.6 - - + -
105B ILE* 3.7 19.3 - - + +
108B PHE* 3.5 28.3 - + + +
109B GLU 2.8 30.5 + - - -
110B GLU* 4.2 2.0 - - + -
112B SER 3.4 16.1 + - - -
116B MET* 4.1 18.9 + - + +
140B ILE* 4.0 14.4 - - + -
141B PRO* 2.9 23.8 + - + +
143B ALA* 1.3 76.7 - - - +
145B VAL* 1.3 64.3 + - - +
146B LYS 3.1 2.0 - - - -
147B THR* 2.8 41.5 + - + -
148B PHE* 3.2 30.2 - + - -
320B MET* 4.0 6.5 - - + -
146O LYS* 5.6 1.3 - - - -
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Residues in contact with VAL 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ILE* 3.6 30.5 - - + +
141B PRO 2.9 20.0 + - - +
142B PRO* 3.6 8.7 - - + +
144B TYR* 1.3 74.6 - - - +
146B LYS* 1.3 64.9 + - + +
148B PHE* 3.1 26.7 + - - +
320B MET* 5.8 0.9 - - - -
367B ASP 4.0 10.8 - - - +
368B TRP* 3.4 37.2 - - + +
369B SMC 4.7 4.5 - - + +
371B MET* 3.6 26.8 - - + +
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Residues in contact with LYS 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142B PRO 3.0 21.2 + - - +
143B ALA 4.2 4.3 - - - +
144B TYR 3.1 0.6 - - - -
145B VAL* 1.3 78.4 - - + +
147B THR* 1.3 60.7 + - + +
148B PHE 3.2 5.9 + - - +
369B SMC 4.2 31.2 + - + +
105O ILE* 4.1 26.7 + - + +
106O ASP* 5.3 1.6 + - - -
108O PHE 5.2 1.2 + - - -
110O GLU* 3.0 46.7 + - - +
143O ALA* 3.4 29.8 - - + +
144O TYR* 5.6 1.1 - - - -
147O THR* 3.6 21.4 - - + +
210V PRO* 3.8 18.0 - - - +
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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