Contacts of the helix formed by residues 140 - 145 (chain B) in PDB entry 4U7C
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 ASN 140 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ALA* 4.3 7.6 - - + -
113B ALA* 3.9 8.8 - - + +
117B MET* 4.0 26.4 - - + +
126B LYS 2.7 29.5 + - - -
128B ILE* 3.2 26.5 + - + +
139B SER* 1.3 76.8 - - - +
141B TYR* 1.3 58.7 + - + +
142B HIS* 3.5 11.6 - - + +
143B ALA* 2.7 37.1 + - - +
144B ARG* 2.8 22.4 + - - +
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Residues in contact with TYR 141 (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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109B ASP* 4.4 1.5 + - + -
110B ALA* 3.6 29.5 + - + -
140B ASN* 1.3 71.4 - - + +
142B HIS* 1.3 66.1 + - - +
144B ARG* 3.4 30.6 + - + +
145B ARG* 2.9 24.4 + - - +
328B LYS* 3.7 15.4 - - + +
329B PRO* 3.6 47.6 - - + +
603B 0KX 2.4 27.3 + - - -
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Residues in contact with HIS 142 (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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117B MET* 6.0 1.8 - - + +
124B LYS 4.7 4.0 + - - -
125B ASP* 3.5 37.8 + - + -
126B LYS 3.9 5.8 + - - +
127B PRO* 4.1 13.5 - - + -
140B ASN* 3.4 20.8 + - + +
141B TYR* 1.3 79.7 - - - +
143B ALA* 1.3 56.8 + - - +
145B ARG* 3.7 8.5 - - - +
146B PHE* 3.4 27.0 - + - -
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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
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127B PRO* 3.8 17.7 - - + -
128B ILE 3.7 14.1 - - - +
139B SER* 4.3 0.9 - - - -
140B ASN* 2.7 22.8 + - - +
142B HIS* 1.3 70.5 - - - +
144B ARG* 1.3 54.5 + - - +
145B ARG 2.9 6.1 - - - -
146B PHE* 2.8 25.6 + - + +
148B VAL* 3.3 30.0 + - + +
161B CYS* 5.5 0.4 - - - -
164B LEU* 4.0 11.9 - - + -
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Residues in contact with ARG 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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110B ALA* 3.9 4.8 - - - +
138B THR* 3.3 13.5 + - - -
139B SER* 3.1 30.9 + - - +
140B ASN 2.8 11.8 + - - +
141B TYR* 3.0 41.6 + - + +
143B ALA* 1.3 76.0 - - - +
145B ARG* 1.3 58.3 + - - +
146B PHE 3.1 0.9 - - - -
147B GLY* 3.3 11.9 + - - -
148B VAL 3.4 19.3 + - - +
149B ARG* 5.1 5.1 - - + +
603B 0KX 2.9 53.4 + - - -
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Residues in contact with ARG 145 (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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31B LEU* 4.6 18.0 + - - +
36B ILE* 5.5 0.7 - - - +
141B TYR 2.9 9.6 + - - +
142B HIS* 3.7 16.4 - - - +
143B ALA 2.9 0.6 - - - -
144B ARG* 1.3 78.6 - - - +
146B PHE* 1.3 64.7 + - + +
147B GLY 3.4 0.8 + - - -
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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