Contacts of the helix formed by residues 112 - 120 (chain B) in PDB entry 3I58
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 GLU 112 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 2.6 32.5 + - - -
109B GLY 3.0 8.9 + - - +
110B PHE 2.8 1.4 - - - -
111B VAL* 1.3 90.2 - - + +
113B LEU* 1.3 64.4 + - - +
114B ALA* 3.1 3.8 - - - -
115B HIS* 2.9 22.0 + - + +
123B ALA* 3.5 18.4 - - + +
126B VAL* 3.7 37.0 - - + +
127B ARG* 4.1 18.1 + - + +
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Residues in contact with LEU 113 (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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17A ALA 4.6 2.7 - - - +
20A MET* 3.9 8.9 - - + +
21A ALA* 3.8 36.6 - - + +
24A VAL* 4.0 11.9 - - + -
58A LEU* 4.2 9.9 - - + -
109B GLY 4.0 0.2 + - - -
110B PHE* 2.8 35.5 + - + +
111B VAL 3.4 1.0 - - - -
112B GLU* 1.3 76.7 - - - +
114B ALA* 1.3 65.1 + - - +
116B SER* 2.7 17.6 + - - +
117B ILE* 3.0 31.1 + - + +
123B ALA* 4.6 5.8 - - - -
288B LEU* 4.8 9.9 - - + -
291B LEU* 4.9 3.1 - - + -
292B THR* 3.9 17.9 - - + -
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A MET* 5.7 0.4 - - - +
24A VAL* 3.5 27.2 - - + +
27A THR* 6.1 1.8 - - + -
28A LEU* 6.3 1.1 - - + -
99A MET* 4.1 20.3 - - + +
112B GLU* 3.1 2.4 - - - +
113B LEU* 1.3 78.2 - - - +
115B HIS* 1.3 62.5 + - - +
117B ILE* 3.1 2.4 + - - +
118B ARG* 2.9 52.2 + - - +
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Residues in contact with HIS 115 (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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112B GLU* 2.9 17.1 + - + +
114B ALA* 1.3 79.2 - - - +
116B SER* 1.3 57.0 + - - +
118B ARG* 3.5 5.3 + - - +
119B THR* 2.8 64.7 + - + +
121B GLN* 3.8 13.4 - - + +
122B PRO 3.5 17.5 + - - -
126B VAL* 3.3 36.1 - - + +
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Residues in contact with SER 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A SER* 3.4 5.5 + - - -
112B GLU 3.7 0.2 + - - -
113B LEU* 2.7 22.7 + - - -
115B HIS* 1.3 73.0 - - - +
117B ILE* 1.3 60.9 + - - -
120B GLY* 2.7 29.9 + - - +
121B GLN 2.6 25.8 + - - -
122B PRO* 3.5 1.2 - - - +
123B ALA* 3.2 24.7 + - - +
291B LEU* 4.0 21.7 + - - +
292B THR* 4.0 5.0 - - - -
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Residues in contact with ILE 117 (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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24A VAL* 4.0 18.6 - - + -
28A LEU* 3.7 27.6 - - + -
50A ALA* 3.5 1.8 - - + +
51A HIS* 3.0 27.0 + - - +
54A SER* 3.8 21.2 - - - +
55A LEU* 4.0 22.2 - - + -
58A LEU* 4.0 17.3 - - + -
113B LEU* 3.0 33.7 + - + +
114B ALA 3.1 5.6 + - - +
116B SER* 1.3 76.7 - - - +
118B ARG* 1.3 58.1 + - - +
288B LEU* 4.7 2.2 - - + -
291B LEU* 4.0 14.1 - - + -
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Residues in contact with ARG 118 (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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27A THR* 3.9 25.7 + - - +
28A LEU* 4.0 26.6 - - + +
48A ALA 5.7 1.2 + - - +
49A GLY 4.1 16.3 - - - +
50A ALA* 3.8 7.7 - - + +
51A HIS* 3.2 19.9 + - - +
100A ASN* 5.0 7.5 + - - +
114B ALA* 2.9 37.1 + - - +
115B HIS* 4.0 5.1 - - - +
117B ILE* 1.3 79.3 - - - +
119B THR* 1.3 66.1 + - + +
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Residues in contact with THR 119 (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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51A HIS* 3.8 13.6 + - - -
115B HIS* 2.8 40.6 + - + +
118B ARG* 1.3 87.0 - - + +
120B GLY* 1.3 56.6 + - - +
121B GLN* 3.0 36.4 + - - +
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Residues in contact with GLY 120 (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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51A HIS* 3.7 15.6 - - - +
54A SER* 3.1 24.9 - - - -
116B SER 2.7 14.7 + - - -
119B THR* 1.3 72.7 - - - +
121B GLN* 1.3 68.2 + - - +
122B PRO* 4.2 0.9 - - - +
291B LEU* 4.0 12.5 - - - +
295B GLY* 4.6 6.4 - - - +
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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