Contacts of the helix formed by residues 139 - 150 (chain T) in PDB entry 1I84
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 139 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101T GLY 2.9 22.6 + - - -
131T HIS* 4.4 2.6 + - - +
138T ILE* 1.3 75.1 - - - +
140T TYR* 1.3 65.2 + - - +
141T GLU* 3.1 26.0 - - - +
142T GLU* 3.0 40.7 + - + +
143T LEU* 3.1 9.9 + - - +
389V HIS* 5.1 0.9 - - - +
392V GLY* 3.5 12.8 - - - -
617V SER* 1.6 43.3 + - - +
618V ASP* 5.5 0.9 - - - +
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Residues in contact with TYR 140 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T VAL* 4.5 9.9 - - + -
92T LEU* 4.0 29.6 - - + -
93T ARG* 3.5 13.5 + - + -
101T GLY 3.7 2.7 - - - -
103T VAL* 3.2 27.5 - - + +
108T ILE* 6.0 1.3 - - + -
138T ILE* 3.7 6.4 + - - +
139T ASN* 1.3 69.4 - - - +
141T GLU* 1.3 111.0 + - + +
142T GLU 2.5 2.6 + - - -
143T LEU* 2.7 12.1 + - + -
144T VAL* 2.6 27.9 + - + +
393V ILE 2.2 18.7 + - - -
394V ASN* 1.7 76.7 - - + -
395V VAL 2.7 2.6 + - - -
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Residues in contact with GLU 141 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T PHE* 3.0 17.4 - - - -
89T VAL* 4.5 9.0 - - - +
93T ARG* 5.1 1.7 + - - -
139T ASN* 3.1 23.3 - - - +
140T TYR* 1.3 109.2 + - + +
142T GLU* 1.3 51.0 + - - +
144T VAL* 3.3 3.3 - - - +
145T ARG* 2.8 36.0 + - - +
385V GLN 4.4 4.5 - - - +
388V CYS* 3.7 2.3 - - - +
389V HIS* 1.8 90.2 + - + +
393V ILE 4.3 1.1 - - - +
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Residues in contact with GLU 142 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131T HIS* 5.7 4.3 - - + -
139T ASN* 3.0 28.7 + - + +
140T TYR 2.5 3.8 + - - -
141T GLU* 1.3 73.9 - - - +
143T LEU* 1.3 68.0 + - - +
144T VAL 2.9 1.3 - - - -
145T ARG* 2.7 50.9 + - - +
146T MET* 2.7 13.5 + - - +
389V HIS* 4.2 3.6 - - - -
617V SER* 4.8 0.9 - - - +
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Residues in contact with LEU 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S PHE* 4.3 22.2 - - + -
92T LEU* 4.6 7.6 - - + -
108T ILE* 4.5 21.1 - - + -
127T LEU* 4.3 16.6 - - + -
128T VAL* 4.2 33.9 - - + -
131T HIS* 4.5 19.8 - - + -
138T ILE* 4.1 19.1 - - + -
139T ASN 3.1 8.0 + - - +
140T TYR* 2.7 11.7 + - - +
142T GLU* 1.3 74.1 - - - +
144T VAL* 1.3 52.2 + - - +
146T MET* 3.3 15.9 - - - +
147T VAL* 2.8 37.5 + - + +
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Residues in contact with VAL 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
799S PHE* 4.7 9.4 - - + -
85T PHE* 3.1 31.9 - - + -
88T TYR* 4.7 7.9 - - + -
89T VAL* 3.3 35.4 - - + +
92T LEU* 4.8 9.9 - - + -
140T TYR* 2.6 23.1 + - + +
141T GLU 3.3 9.0 - - - +
143T LEU* 1.3 73.8 - - - +
145T ARG* 1.3 66.7 + - - +
147T VAL* 3.1 8.4 - - - +
148T LEU* 2.9 36.4 + - + +
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Residues in contact with ARG 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85T PHE* 2.9 36.6 - - + -
141T GLU* 2.8 19.1 + - - +
142T GLU* 2.7 34.7 + - - +
144T VAL* 1.3 74.5 - - - +
146T MET* 1.3 57.1 + - - +
148T LEU* 4.0 6.5 - - - -
149T SER* 2.7 41.1 + - - +
389V HIS* 1.1 81.2 + - - -
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Residues in contact with MET 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806S TYR* 3.0 50.8 - - + +
126T GLN 5.7 0.7 - - - +
127T LEU* 3.8 14.6 - - - +
131T HIS* 3.2 39.9 - - + +
142T GLU 2.7 14.9 + - - +
143T LEU* 3.3 24.7 - - - +
145T ARG* 1.3 72.6 - - - +
147T VAL* 1.3 72.9 + - - +
150T GLY* 2.9 19.6 + - - +
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Residues in contact with VAL 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S PHE* 3.8 26.2 - - + -
802S GLN* 4.7 7.8 - - - +
803S CYS* 4.0 14.1 - - - -
806S TYR* 3.1 49.9 - - + +
809S ARG* 5.6 2.8 + - - -
127T LEU* 3.5 26.9 - - + -
143T LEU* 2.8 22.7 - - + +
144T VAL 3.1 10.3 - - - +
146T MET* 1.3 77.5 - - + +
148T LEU* 1.3 68.4 + - + +
150T GLY 3.9 1.6 - - - -
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Residues in contact with LEU 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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799S PHE* 5.3 3.8 - - + -
802S GLN* 3.9 29.2 - - + +
809S ARG* 5.7 1.9 + - - -
84T CYS* 4.6 3.1 - - - -
85T PHE* 3.9 29.4 - - + +
88T TYR* 4.0 22.4 - - + -
144T VAL* 2.9 33.0 + - + +
145T ARG* 3.0 6.7 + - - +
147T VAL* 1.3 87.0 - - + +
149T SER* 1.3 56.9 + - - +
150T GLY 2.6 22.2 + - - +
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Residues in contact with SER 149 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145T ARG* 2.7 21.0 + - - +
148T LEU* 1.3 73.6 - - - +
150T GLY* 1.3 63.0 + - - +
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Residues in contact with GLY 150 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806S TYR* 3.8 18.2 - - - -
809S ARG* 4.9 17.4 + - - -
810S LYS* 4.4 16.8 - - - -
146T MET* 2.9 20.4 + - - +
147T VAL 3.9 6.5 - - - -
148T LEU 2.6 15.7 + - - +
149T SER* 1.3 82.9 - - - +
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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