Contacts of the helix formed by residues 109 - 118 (chain A) in PDB entry 3K57
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 ARG 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A TRP* 4.2 17.8 - - + +
86A HIS* 3.2 23.4 + - - -
87A ARG* 5.2 2.0 - - - +
90A MET* 3.1 35.0 - - - +
106A ALA 4.6 1.0 + - - -
107A ASP* 3.2 31.6 + - - +
108A VAL* 1.3 75.3 - - - +
110A PRO* 1.3 69.1 - - + +
111A PRO* 3.5 3.1 - - + -
112A GLU* 3.3 27.0 + - - +
113A ARG* 2.9 26.1 + - - +
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Residues in contact with PRO 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TRP* 3.8 18.8 - - + +
19A THR* 4.1 10.3 - - + -
21A VAL* 3.7 24.3 - - + +
39A GLN* 5.2 6.9 - - + +
41A SER* 4.2 5.6 - - - +
86A HIS* 3.7 36.6 - - + +
108A VAL 3.9 0.6 - - - +
109A ARG* 1.3 86.2 - - + +
111A PRO* 1.3 72.2 - - + +
113A ARG* 3.3 7.0 + - + +
114A TYR* 3.1 23.2 + - - +
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Residues in contact with PRO 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 3.9 22.4 - - + -
11A HIS 3.5 28.3 - - - +
12A TRP* 3.4 18.4 - - + -
21A VAL* 4.0 12.8 - - + -
23A PHE* 3.9 10.0 - - + -
109A ARG* 3.5 0.4 - - + -
110A PRO* 1.3 100.5 - - + +
112A GLU* 1.3 76.6 + - - +
114A TYR* 3.3 2.5 + - + +
115A LEU* 3.2 29.3 + - - +
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Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ARG* 4.3 20.2 - - - +
108A VAL* 4.6 3.1 - - + -
109A ARG* 3.3 22.4 + - - +
111A PRO* 1.3 93.9 - - - +
113A ARG* 1.3 63.1 + - - +
115A LEU* 4.7 5.8 - - - +
116A MET* 2.9 50.1 + - + +
375A HIS* 4.6 10.2 + - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A GLU 5.7 4.5 - - - +
42A VAL* 3.0 48.2 + - + +
44A PHE* 4.2 3.7 - - - -
105A GLU* 2.8 49.7 + - - +
108A VAL* 3.7 30.9 + - + +
109A ARG 2.9 17.6 + - - +
110A PRO* 3.6 9.0 - - + +
111A PRO 3.3 0.2 - - - -
112A GLU* 1.3 76.1 - - - +
114A TYR* 1.3 63.1 + - - +
116A MET* 3.9 4.3 - - - +
117A GLU* 3.3 39.1 + - + +
378A PHE* 4.3 4.4 - - - -
382A HIS* 4.0 12.3 - - - -
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Residues in contact with TYR 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 5.2 0.2 - - + -
23A PHE* 4.3 4.0 - + + -
36A LEU* 3.7 39.2 - - + +
39A GLN* 3.7 23.8 - - + +
110A PRO 3.1 9.6 + - - +
111A PRO* 3.6 8.3 - - + +
113A ARG* 1.3 84.4 - - - +
115A LEU* 1.3 75.7 + - + +
117A GLU* 3.8 2.1 + - - +
118A ARG* 3.2 68.3 + - + +
138A ALA 4.2 1.4 + - - -
139A ARG* 3.6 8.3 - - - -
140A LEU* 3.1 42.5 + - + -
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Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 3.8 20.2 - - + -
10A ARG* 3.6 25.1 - - - +
23A PHE* 3.5 32.3 - - + -
111A PRO 3.2 15.7 + - - +
112A GLU* 4.1 3.8 - - - +
114A TYR* 1.3 85.3 - - + +
116A MET* 1.3 61.7 + - - +
118A ARG 3.0 7.1 + - - -
120A ILE* 2.9 68.3 + - + +
121A THR 4.4 5.8 - - - +
140A LEU* 4.2 5.4 - - + -
375A HIS* 4.4 6.5 - - - +
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Residues in contact with MET 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A VAL* 4.0 15.7 - - + -
112A GLU* 2.9 46.9 + - + +
113A ARG* 3.9 4.5 - - - +
115A LEU* 1.3 77.2 - - - +
117A GLU* 1.3 65.1 + - - +
119A PHE* 3.2 11.8 + - - -
374A GLY 4.3 4.9 - - - +
375A HIS* 3.5 50.1 + - + +
378A PHE* 3.5 43.7 - - + -
379A PRO* 3.2 20.2 - - + +
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.3 34.0 + - + +
114A TYR* 4.2 3.4 - - - +
115A LEU 3.3 0.2 - - - -
116A MET* 1.3 80.7 - - + +
118A ARG* 1.3 60.2 + - + +
119A PHE* 3.3 2.3 + - - -
378A PHE* 4.1 4.3 - - - +
379A PRO* 3.9 12.0 - - - +
382A HIS* 2.6 39.5 + - - +
383A ARG* 3.1 49.5 + - - -
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Residues in contact with ARG 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.2 56.3 + - - +
115A LEU 3.0 9.3 + - - +
117A GLU* 1.3 82.5 - - + +
119A PHE* 1.3 73.4 + - - +
120A ILE* 3.1 10.1 - - + -
139A ARG* 4.5 10.1 - - - +
140A LEU 2.6 39.9 + - - +
141A LYS* 4.8 3.4 - - - +
142A PRO* 3.2 18.3 - - + +
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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