Contacts of the strand formed by residues 106 - 112 (chain A) in PDB entry 3IOT
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 TYR 106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A ILE* 3.4 48.1 - - + +
80A THR 4.4 1.2 + - - -
81A PRO* 4.1 17.0 - - + -
85A PHE* 4.5 5.8 - + - -
94A TRP* 4.0 12.6 - + - -
105A ALA* 1.3 71.7 - - - +
107A PRO* 1.3 67.8 - - + +
108A ILE* 3.6 3.2 + - + +
263A SER* 3.1 4.0 - - - -
264A ALA* 2.7 45.0 + - + +
266A ILE* 4.9 2.2 - - + -
277A LYS* 3.7 20.5 - - - +
280A LEU* 3.6 42.6 - - + -
281A GLU* 3.0 30.9 + - + +
285A LEU* 3.9 20.4 - - + -
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Residues in contact with PRO 107 (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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89A LEU* 3.7 12.1 - - + +
93A THR* 3.7 45.3 - - - +
94A TRP* 3.5 22.2 - - + -
97A VAL* 3.8 9.2 - - + -
105A ALA 3.7 3.1 - - - +
106A TYR* 1.3 85.9 - - - +
108A ILE* 1.3 66.5 + - - +
261A VAL* 4.2 11.7 - - + -
262A LEU 3.8 4.9 - - - +
263A SER* 4.4 3.8 - - - +
285A LEU* 3.7 15.8 - - - +
303A ALA* 3.8 13.2 - - + +
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Residues in contact with ILE 108 (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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61A PHE* 3.9 32.8 - - + -
106A TYR* 3.7 12.3 - - + +
107A PRO* 1.3 83.5 - - - +
109A ALA* 1.3 63.9 + - + +
261A VAL* 4.4 0.6 - - - +
262A LEU* 2.6 35.8 + - + +
263A SER* 4.0 0.9 - - - -
264A ALA* 4.0 9.0 - - + +
280A LEU* 5.6 0.4 - - + -
284A LEU* 4.2 14.8 - - + -
285A LEU* 4.4 17.1 - - + +
290A LEU* 4.4 20.5 - - + +
299A LEU* 4.8 9.6 - - + -
302A VAL* 3.6 8.3 - - - +
303A ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 109 (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 ILE* 1.3 85.3 - - + +
110A VAL* 1.3 64.5 + - - +
111A GLU* 5.5 0.2 - - - +
260A GLY 3.9 0.5 - - - +
261A VAL* 3.2 7.5 - - - +
262A LEU* 2.9 37.1 + - + +
299A LEU* 3.3 38.4 - - + +
301A ALA 3.2 7.2 - - - +
302A VAL* 4.1 1.6 - - + +
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Residues in contact with VAL 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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92A PHE* 4.4 5.6 - - + -
93A THR* 4.1 24.2 - - + -
109A ALA* 1.3 77.0 - - - +
111A GLU* 1.3 65.1 + - - +
229A PRO* 5.6 0.3 - - - +
259A VAL* 3.6 15.9 - - + -
260A GLY 3.9 1.6 - - - -
261A VAL* 4.3 7.6 - - + -
299A LEU 4.5 3.3 - - - +
300A GLY* 5.0 0.7 - - - -
301A ALA* 2.7 32.0 + - + +
302A VAL 4.4 9.0 - - - -
303A ALA* 4.4 1.3 - - + +
320A THR* 4.1 5.3 - - + +
321A MET* 3.7 27.6 - - + -
324A ALA* 3.6 31.4 - - + -
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Residues in contact with GLU 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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15A LYS* 5.1 8.5 + - - -
110A VAL* 1.3 78.0 - - - +
112A ALA* 1.3 62.5 + - - +
155A TYR* 4.9 3.9 + - - -
229A PRO* 3.8 24.9 - - + +
230A TRP* 3.5 35.0 + - + +
258A PHE 3.8 0.5 - - - +
259A VAL* 3.4 6.9 - - - -
260A GLY* 2.8 48.3 + - - +
320A THR* 4.5 1.6 - - - -
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Residues in contact with ALA 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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111A GLU* 1.3 79.3 - - - +
113A LEU* 1.3 69.8 + - - +
114A SER* 3.7 7.4 + - - -
155A TYR* 4.8 3.1 - - - -
228A GLY* 4.2 0.4 - - - -
229A PRO* 3.8 18.0 - - - +
230A TRP* 5.5 0.4 - - - -
257A PRO* 4.6 4.0 - - + -
258A PHE 3.9 15.0 - - - +
259A VAL* 4.8 0.9 - - + -
320A THR* 3.8 17.7 + - - +
323A ASN 4.4 1.8 - - - -
324A ALA* 3.8 33.9 - - + +
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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