Contacts of the helix formed by residues 137 - 147 (chain T) in PDB entry 3P71
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 137 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52T GLN 4.8 2.6 + - - -
53T HIS* 3.2 53.9 + - + +
132T HIS* 5.7 5.2 - - - -
133T SER* 3.1 25.5 + - - +
134T ILE 3.2 7.2 - - - +
135T LYS 3.4 0.8 - - - -
136T CYS* 1.3 88.1 - - + +
138T PRO* 1.3 63.0 - - + +
139T PRO* 3.3 8.3 - - + -
140T LEU* 2.9 25.9 + - + +
141T SER* 3.2 10.0 + - - -
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Residues in contact with PRO 138 (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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135T LYS 5.5 0.2 - - - +
136T CYS 3.4 11.2 - - - +
137T LYS* 1.3 78.4 - - - +
139T PRO* 1.4 71.8 - - + +
140T LEU 2.9 5.3 + - - -
141T SER* 3.4 12.6 - - - +
142T SER* 2.9 39.9 + - - +
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Residues in contact with PRO 139 (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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50T TYR* 4.3 12.5 - - + -
53T HIS* 3.6 35.2 - - + +
106T TRP* 4.1 5.0 - - - -
137T LYS* 3.5 6.7 - - + -
138T PRO* 1.4 96.9 - - + +
140T LEU* 1.3 57.6 + - - +
142T SER* 5.5 0.4 - - - -
143T PRO* 3.4 21.6 - - + +
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Residues in contact with LEU 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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50T TYR* 4.4 9.2 - - + +
53T HIS* 3.8 36.8 - - + -
54T PHE* 3.7 39.9 - - + -
106T TRP* 2.8 39.3 + - + +
133T SER* 3.2 32.8 - - - +
134T ILE* 3.8 10.3 - - - +
137T LYS* 2.9 10.6 + - + +
138T PRO 2.9 0.4 - - - -
139T PRO* 1.3 80.3 - - - +
141T SER* 1.3 60.7 + - - +
142T SER 3.6 0.7 - - - -
143T PRO* 3.6 1.8 - - - +
144T ILE* 3.3 14.6 - - - +
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Residues in contact with SER 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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134T ILE* 3.4 17.2 + - - -
135T LYS* 4.8 6.3 + - - -
137T LYS 3.2 3.9 + - - -
138T PRO* 3.0 18.2 + - - +
140T LEU* 1.3 76.9 - - - +
142T SER* 1.3 68.8 + - - +
144T ILE* 3.3 10.8 + - - +
145T LEU* 3.0 33.8 + - - +
153T LEU* 4.1 17.4 - - - +
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Residues in contact with SER 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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138T PRO* 2.9 24.5 + - - +
139T PRO* 5.5 0.2 - - - -
141T SER* 1.3 78.4 + - - +
143T PRO* 1.4 59.2 - - - +
145T LEU* 3.0 11.5 + - - +
146T GLU* 2.7 49.6 + - - +
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Residues in contact with PRO 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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50T TYR* 5.5 4.0 - - + +
105T PHE* 4.6 3.0 - - + -
106T TRP* 3.8 21.8 - - + -
109T LYS* 3.3 41.1 - - + -
138T PRO 3.7 0.2 - - - +
139T PRO* 3.4 26.5 - - + +
140T LEU 3.6 5.6 - - - +
142T SER* 1.4 95.1 - - - +
144T ILE* 1.3 60.0 + - - +
146T GLU* 3.7 13.7 + - - +
147T LEU* 3.7 9.9 + - - +
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Residues in contact with ILE 144 (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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105T PHE* 3.9 17.5 - - + -
106T TRP* 3.8 13.5 - - + +
134T ILE* 3.9 21.1 - - + -
140T LEU 3.3 21.8 - - - +
141T SER* 3.3 5.6 + - - +
142T SER 3.2 0.6 - - - -
143T PRO* 1.3 76.7 - - - +
145T LEU* 1.3 62.1 + - - +
147T LEU* 3.4 5.9 + - - +
148T HIS* 3.2 18.7 + - - +
153T LEU* 3.6 22.0 - - + -
160T LEU* 4.9 2.7 - - + -
162T SER* 3.5 24.2 + - - +
164T ARG* 6.0 0.7 + - - +
165T TYR* 3.6 35.7 - - + -
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Residues in contact with LEU 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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141T SER* 3.0 28.0 + - - +
142T SER* 3.0 7.9 + - - +
144T ILE* 1.3 74.0 - - - +
146T GLU* 1.3 62.9 + - - +
147T LEU 2.9 4.9 - - - -
148T HIS* 2.9 22.5 + - + +
150T GLU 3.8 11.0 - - - +
151T ASP* 3.5 35.7 - - - +
152T THR 3.9 1.3 - - - -
153T LEU* 3.7 35.9 - - + +
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Residues in contact with GLU 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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109T LYS* 2.9 28.5 + - - +
142T SER* 2.7 33.8 + - - +
143T PRO* 3.8 12.7 - - - +
144T ILE 3.4 0.4 - - - -
145T LEU* 1.3 71.8 - - - +
147T LEU* 1.3 64.2 + - + +
148T HIS 4.8 1.7 - - - +
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Residues in contact with LEU 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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105T PHE* 4.2 8.3 - - + -
109T LYS* 3.7 27.1 - - + +
114T LEU* 3.4 32.8 - - + -
143T PRO 3.7 7.8 + - - +
144T ILE* 3.4 9.7 + - - +
145T LEU 2.9 0.6 - - - -
146T GLU* 1.3 82.3 - - + +
148T HIS* 1.3 61.3 + - - +
163T LYS* 3.6 18.6 - - - +
164T ARG* 3.6 38.5 - - + +
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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