Contacts of the strand formed by residues 105 - 111 (chain B) in PDB entry 3IO6
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 ALA 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B PHE* 3.6 33.0 - - + -
79B ILE* 3.4 21.3 - - - +
94B TRP* 4.0 0.3 - - - -
97B VAL* 3.4 36.5 + - + +
103B LEU 3.8 0.4 - - - -
104B ILE* 1.3 83.4 - - + +
106B TYR* 1.3 59.6 - - - +
107B PRO* 3.8 1.0 - - - +
263B SER* 4.1 1.3 - - - -
264B ALA 3.3 13.9 - - - +
265B GLY* 4.0 0.7 - - - -
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Residues in contact with TYR 106 (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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79B ILE* 3.4 45.9 - - + +
80B THR 4.2 0.3 + - - -
81B PRO* 4.1 10.9 - - + -
85B PHE* 3.7 32.5 - + - -
94B TRP* 4.3 5.2 - + - -
105B ALA* 1.3 73.0 - - - +
107B PRO* 1.3 66.2 - - + +
108B ILE* 3.5 7.0 + - + +
263B SER* 3.1 4.0 - - - -
264B ALA* 2.6 43.5 + - + +
266B ILE* 4.2 11.4 - - + +
277B LYS* 3.6 13.9 - - + +
280B LEU* 3.8 28.7 - - + -
281B GLU* 2.9 29.7 + - + -
285B LEU* 3.9 18.4 - - + -
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Residues in contact with PRO 107 (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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89B LEU* 3.7 20.8 - - + +
93B THR* 3.5 43.3 - - - +
94B TRP* 3.6 20.4 - - + -
97B VAL* 3.8 9.4 - - + -
105B ALA 3.8 1.7 - - - +
106B TYR* 1.3 84.6 - - + +
108B ILE* 1.3 60.3 - - - +
261B VAL* 4.0 9.0 - - + -
262B LEU 3.9 0.9 - - - +
263B SER* 3.8 9.8 - - - -
285B LEU* 3.6 15.4 - - - +
303B ALA* 3.4 14.1 - - + +
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Residues in contact with ILE 108 (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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61B PHE* 3.7 33.2 - - + -
106B TYR* 3.6 18.2 - - + +
107B PRO* 1.3 72.3 - - - +
109B ALA* 1.3 57.6 + - + +
261B VAL* 4.5 0.4 - - - +
262B LEU* 2.7 24.1 + - + +
263B SER* 4.0 5.2 - - - -
264B ALA* 4.5 4.3 - - + -
280B LEU* 4.8 1.1 - - + -
284B LEU* 4.4 10.5 - - + -
285B LEU* 3.7 29.3 - - + +
290B LEU* 3.9 26.0 - - + +
299B LEU* 4.0 14.8 - - + -
302B VAL* 3.6 5.1 - - - +
303B ALA* 2.7 33.9 + - - +
304B LEU 4.7 0.3 + - - -
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Residues in contact with ALA 109 (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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108B ILE* 1.3 79.5 - - - +
110B VAL* 1.3 63.5 + - - +
111B GLU* 5.8 0.2 - - - -
260B GLY 3.9 0.2 - - - +
261B VAL* 3.3 7.3 - - - +
262B LEU* 2.8 48.8 + - + +
299B LEU* 3.7 36.1 - - + +
301B ALA 3.4 8.7 - - - +
302B VAL* 4.4 0.9 - - - +
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Residues in contact with VAL 110 (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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92B PHE* 3.9 9.0 - - + -
93B THR* 4.0 24.5 - - + -
109B ALA* 1.3 77.7 - - - +
111B GLU* 1.3 63.9 + - - +
229B PRO* 5.8 0.3 - - - +
259B VAL* 3.7 25.4 - - + -
260B GLY 3.7 1.8 - - - -
261B VAL* 4.4 4.7 - - + -
299B LEU 4.6 3.5 - - - +
300B GLY* 5.1 0.3 - - - -
301B ALA* 2.5 46.7 + - + +
303B ALA* 4.3 10.3 - - + +
320B THR* 4.4 4.0 - - + +
321B MET* 4.2 14.4 - - + -
324B ALA* 3.7 22.0 - - + -
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Residues in contact with GLU 111 (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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15B LYS* 5.3 8.5 + - - -
109B ALA 5.8 0.2 - - - -
110B VAL* 1.3 76.6 - - - +
112B ALA* 1.3 66.2 - - - +
155B TYR* 4.9 4.0 + - - +
229B PRO* 4.4 14.3 - - + +
230B TRP* 3.2 42.9 + - + +
258B PHE 3.8 0.9 - - - +
259B VAL* 3.5 4.3 - - - +
260B GLY* 2.8 46.5 + - - +
299B LEU 6.1 0.2 - - - +
320B THR* 4.9 1.6 - - - -
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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